dataesr/scientific-paragraphs-categorization huggingface dataset:
Conclusions This study deals with the fatigue behavior of a woven glass-fibre-reinforced composite with PA66 matrix. Tension-tension fatigue tests were performed on open-hole samples. These tests were instrumented with acoustic emission and infrared thermography. Monitored data have highlighted a damage accumulation around the hole, identified as fibre-matrix debonding and fibre breakages. A fatigue life model was applied on openhole sample, with material parameters determined on plain samples. Results show a slight underestimation of the fatigue life. In addition, 3-point bending fatigue tests were performed on automotive mini-structures. The fatigue life model tested on open-hole samples were also applied on ministructure. As a reminder, the inputs needed for the use of this model are: -A Wöhler curve obtained on rectangular samples tested in 3-point bending ; -A numerical model of the mini-structure ; -A monotonic 3-point bending test for the validation of the numerical model ; With these data, it is then possible to estimate the fatigue life of the mini-structure in 3-point bending mode.
Two of the latter clades are represented by A. baumannii strain K50 and A. baumannii AA-014 (GenBank accession no. GCA_000335595. 1) as well as A. baumannii SDF (GenBank accession no. GCA_000069205. 1), respectively. Hence, A. baumannii strain K50 appeared to be located outside the CC1 and CC2 clusters but is actually closely related to A. baumannii strain AA-014. To determine the ST of strain K50, multilocus sequence typing (MLST) revealed that strain K50 belongs to sequence type 158 according to the Pasteur scheme and ST499 according to the Oxford scheme. A. baumannii strain AA-014 also is a member of ST158 (Pasteur scheme) and ST499 (Oxford scheme). The latter strain was sequenced in the frame of the Genomic Sequencing of a Diversity of US Military Acinetobacter baumannii/A. calcoaceticus Complex Isolates project.
Moreover, multiple genes for multidrug efflux pumps and ABC transporters potentially mediate resistance to fluoroquinolones and macrolides, among other compounds. These and other resistance genes in the chromosome of strain K50 are listed in Table  S1  in the supplemental material. Genes potentially involved in virulence were identified by comparisons to the Virulence Factor Database (VFDB)  (20). It appeared that A. baumannii strain K50 possesses different virulence genes featuring predicted functions in adherence, biofilm formation, immune evasion, and iron uptake, among others (Table  S2 ). A. baumannii commonly synthesizes capsular polysaccharides and lipooligosaccharides (LOSs) that are involved in virulence and pathogenesis  (21). The corresponding genes are clustered in two loci. Capsule biosynthesis and transport genes are located in the pathogenicity region known as the K locus, encoding enzymes involved in the synthesis and assembly of capsular oligosaccharide repeating units (K antigen).
baumannii genomes. However, these regions are not very frequently represented in other Acinetobacter species and are not present in other bacteria. In contrast, comparative nucleotide sequence analyses with other Acinetobacter sp. genomes disclosed that GI-2 and GI-8 feature unique genetic structures. GI-2 is 13,124 bp and contains 12 putative CDSs comprising mostly hypothetical genes, a tetR transcriptional regulator gene, a NADH oxidase gene, and a metal-dependent hydrolase gene. A similar structure is present in Acinetobacter pittii PHEA-2 (GenBank accession no. CP002177), isolated from industrial wastewater in China (65% coverage and 82% sequence identity), and in Acinetobacter oleivorans DR1 (GenBank accession no. CP002080), a diesel-degrading strain isolated from paddy rice soil from South Korea (27% coverage and 92% sequence identity).
Alignments of these regions are shown in Fig. S2  in the supplemental material. GI-2-flanking regions seem to be conserved among different A. baumannii strains and less conserved than those of other Acinetobacter species. Flank- ing genes generally encode proteins involved in lipid metabolism and/or solventogenesis (not shown). GI-8 comprises 23,659 bp and 19 CDSs (Fig. S2 ). In this region, two gene clusters were identified, one containing mostly hypothetical genes and a second cluster encoding hypothetical proteins probably originating from bacteriophages. Database searches showed that a similar structure is present in A. baumannii strain AB5075-UW (GenBank accession no. NZ_CP008706) (87% coverage and 99% identity). Differences between these regions are restricted to a small segment comprising two CDSs related to phage genes in strain K50 (2,255 bp) and four CDSs encoding hypothetical proteins in strain AB5075-UW (4,299bp) (Fig.
A comparison of prophage regions with the predicted GIs described above revealed the association of GI-5 with region 1, comprising a complete prophage, whereas GI-6 and GI-7 are located in close proximity to prophage region 2. Nucleotide sequence comparison of the latter cluster with other genomes deposited in databases revealed that it is unique but similar to two regions of the A. baumannii BAL062 chromosome (GenBank accession no. NZ_LT594095). However, the similarity between these sequences is due mostly to hypothetical genes rather than phage-related genes. The small putative virulence plasmid pK50b. Plasmid pK50b (9. 5 kb) harbors 13 predicted genes. Five of these genes were annotated as "hypothetical. " Among the genes with predicted functions, two replication initiation genes (rep), one encoding a Rep_3 superfamily protein (PF01051), as well as two type II toxin-antitoxin system genes, namely, relBE and brnTA, were identified.
Moreover, a gene encoding a cholesterol-dependent cytolysin named septicolysin and a TonB-dependent outer membrane receptor gene are present on the plasmid. Septicolysin is a pore-forming toxin  (30) , and the TonB-dependent receptor protein was predicted to be involved in iron acquisition and virulence  (31). Hence, plasmid pK50b harbors two putative virulence determinants. Database searches revealed that plasmid pK50b is highly similar to other A. baumannii plasmids, such as pA85-2 (32) and pAB0057  (33) , which were also isolated from multiresistant strains. However, there are two major differences between pK50b and other related plasmids: (i) the presence of XerD-XerC recombination sites flanking three CDSs, namely, the toxin-antitoxin genes relBE and one hypothetical gene, and (ii) the presence of two rep genes whose sequences are not closely related to those found in similar plasmids (Fig.
The class 1 integron is flanked by miniature inverted-repeat transposable elements (MITEs)  (45, 46) , as described previously for plasmid p1AB5075 (42) and as described recently for pAb8098  (14). The left and right ends of the pK50a integron, including the MITEs and the 5-bp target site duplication, are identical to the integron on plasmid p1AB5075. However, an additional 6-kb fragment on p1AB5075 containing another int1 integrase gene and further antibiotic resistance genes, namely, aadB, cmlA5, aadA2, and strAB, is actually missing on plasmid pK50a. Comparative analyses of A. baumannii pK50a and closely related plasmids. Nucleotide sequence analyses of plasmid pK50a revealed that it is closely related to other plasmids of clinical multiresistant A. baumannii strains, such as p1AB5075 (GenBank accession no.
CP008707) (42), ABKp1 (GenBank accession no. CP001922), pAb-G7-2 (GenBank accession no. KF669606) (47), p2ABTCDC0715 (GenBank accession no. CP002524)  (48) , and pAb8098 (GenBank accession no. KY022424. 1) (14) (see Table  S7  in the supplemental material). To evaluate their genomic relationships, a comparative analysis was performed, as described previously  (49, 50). The results of this analysis are shown in Fig. 5. All plasmids share a backbone composed of homologous regions. These regions account for 76% (plasmid p1AB5075) to 90% (plasmid pAb-G7-2) of the whole plasmid genome sequence. Plasmids p1AB5075, pABKp1, pAb-G7-2, p2ABTCDC0715, pAb8098, and pK50a share 58 genes, namely, the replication initiation gene, 5 stable maintenance genes, 19 conjugative transfer genes, 29 hypothetical genes, and 4 genes encoding miscellaneous functions.
Isolation and transfer of plasmid pK50a. Plasmid DNA was extracted by using the Kieser method (56), and electroporation was performed by using A. baumannii CIP70. 10 as a recipient. For mating experiments, the selection of recipient strains was done on ticarcillin (50 mg/ml) and sodium azide (100 mg/ml) or rifampin (100 mg/ml), depending on the recipient strain used. Sequencing and annotation of the A. baumannii K50 genome. The genome of A. baumannii K50 was sequenced by using the Illumina MiSeq system followed by bioinformatic analyses, as previously described for A. baumannii strains R2090, R2091, and CIP70. 10 (57, 58). In brief, an 8-kb mate pair sequencing library was constructed for strain K50, sequenced, and assembled by using GS de novo Assembler software (version 2. 8; Roche). To facilitate gap closure and assembly validation, a combination of PCR-based and in silico-based strategies was applied  (59).
The three final K50 replicons (the bacterial chromosome and two plasmids) were annotated by means of the Prokka rapid prokaryotic genome annotation tool  (60)  and the GenDB annotation platform  (61) , based on the annotation of the reference strain A. baumannii AB307-0294 (GenBank accession no. CP001172),  (33). In addition, WebMGA was applied for COG annotation, with default settings (E value threshold of 1 3 10 220 )  (62). Moreover, all genes that are discussed in this study were manually annotated with the help of BLAST and other tools, as described recently  (49, 59, 63). Comparative analysis, phylogenetic classification, and multilocus sequence typing. Comparative analyses and phylogenetic classification of A. baumannii strain K50 were performed by using EDGAR 2. 0 (16), as recently described  (57).
The ST of A. baumannii strain K50 was determined by applying data in the A. baumannii MLST database according to the Pasteur scheme (cpn60, fusA, gltA, pyrG, recA, rplB, and rpoB) and the Oxford scheme (gltA, gyrB, gdhB, recA, cpn60, gpi, and rpoD) (https://pubmlst. org/ abaumannii/). To determine the similarity between A. baumannii strain K50 and A. baumannii strain AA-014 as well as between pK50a and the related plasmids p1AB5075, ABKp1, pAb-G7-2, and p2ABTCD0715, an ANI analysis was performed, as described previously  (64, 65). Detection of antibiotic resistance genes and pathogenicity determinants. The prediction of chromosomal antibiotic resistance genes was accomplished by using the ARG-ANNOT  (66)  and GenBank databases, applying default parameters. The identification of virulence and pathogenicity factors was carried out by using VFDB  (20).
ACKNOWLEDGMENTS This work was partially funded by the  University of Fribourg  and by the  Swiss National Science Foundation  (project  FNS-31003A_163432 ). I. P. S. was supported by a  postgraduate fellowship  from  CONICET  and a  DAAD (German Academic Exchange Service ) short-term fellowship. We gratefully acknowledge the bioinformatics support of the  BMBF -funded project  Bielefeld-Gießen Center for Microbial Bioinformatics-BiGi  (grant number  031A533 ) within the  German Network for Bioinformatics Infrastructure (de. NBI).
The atmospheric correction is performed using the SMAC (Simplified Method for Atmospheric Correction) software  (Rahman and Dedieu, 1994). SMAC considers linear parameterizations for the absorption and scattering components of molecules and aerosols based on the physics of the 6S code. These relationships include tunable coefficients depending on aerosol type and PROBA-V channels. However, a continental type is taken everywhere whereas the aerosol optical depth (AOD) at the wavelength of 550 nm is prescribed as a function of latitude. The S1 TOC PROBA-V reflectance is distributed with the Status Map (SM), which tells about the quality of the product (radiometry quality, cloud mask, etc. ) (see Table  1 ). A land sea mask (LSM) is used to delineate the coastline. Note that for time being, the inner water bodies are not masked by the application of LSM.
Age of the product The accumulation of information over days is mandatory for polar orbiting systems. The longer is the composite period, the more data to be stored for further exploitation. This is a trade-off process. Herein, PROBA-V land surface albedo and TOC-R products are reduced to 20-days composite period against 30-days for 1 km VEGETATION program because the 333 m resolution of PROBA-V permits a better cloud removal. The product frequency is still 10 days. The synthetic period ends at days 10, 20, and last day of the month (Fig. 3 ). The true age of the product, Z_Age, is given to the user per pixel as a novelty. It is the median date value of clear sky dates over the composite period. Smoothness is slightly enhanced by assigning weight to the a priori information. Duration of cloudiness entails the propagation of a priori information and gap-filling.
Negative NDVI values combining RED and NIR PROBA-V channels served to distinguish snow from snow-free pixels. The values in Table  3  were initially determined by van Leeuwen and  Roujean (2002)  for VEGETATION, further adapted to PROBA-V by VITO. Linear relationships were calibrated using synthetic data sets generated by the SAIL (Scattering by Arbitrarily Inclined Leaves) radiation transfer code  (Verhoef, 1984) , plus ASTER spectral library  (Hook, 1998). They hold for both DHR (AL-DH) and BHR (AL-BH) products by assuming a spectral irradiance regardless to atmospheric effects. The errors of the spectral albedo estimates are supposed uncorrelated (see Table  3 ). ∑ = + a c c a γ 0 γ β β βγ (9).
Methodology for quality assessment of the product Preliminary Quality Assessment of the PROBA-V 1 Collection 300 m was focused on the surface albedo product merely. The evaluation is carried on over a European region covering the area from 35°to 65°of latitude and from -20°to 30°of longitude. The harnessing lumps together a cross-comparison with MODIS C6 products and then a direct validation using available ground observations coming from European Fluxes Data Cluster (EFDC) stations. The following main criteria were devised: spatial consistency, temporal consistency, and statistical assessment of discrepancies with similar products and accuracy. Surface albedo products receive regularly updated specifications (e. g. GCOS, 2016) as it is the case for an ECV (Essential Climate Variable). For surface albedo values lower than 0.
). It is achieved through systematic visual inspection analysis of the global maps, using the maps difference at a monthly basis. Temporal consistency reports on the degree of realism of the temporal variations. Temporal courses of satellite products were investigated over the confident sites of the EUVAL network and other selected stations. This supposes high frequency data are available like daily ground observations. Statistical analysis was performed over a selection of representative European sites for validation (EUVAL) based on uncertainties metrics associated to the scatter-plots between pairs of products (Table  4 ). To be outlined that only sites that are spatially representative at the kilometer scale were put in valor. Table  5  summarizes the number of validation metrics used to verify the consistency between PROBA-V SA Collection 300 m for the whole 2014 year, using as references MODIS C6 product and ground data coming from EFDC stations.
A trimmed analysis of the spatial and statistical consistency was performed at 1 km resolution. PROBA-V SA 300 m products were resampled using an average value over a 3 × 3 pixels window (from 1/ 3 km to 1 km spatial resolution). MODIS C6 data were re-sampled using an average over 2 × 2 pixels window (from 1/2 km to 1 km). Twofold analysis based on temporal consistency and accuracy assessment relied on the native spatial resolution of each product. The comparison is carried on 10-days periods defined as the closest to the center of the temporal composite window, being 20 days (PROBA-V SA 300 m) and Selected 10 EFDC sites for Accuracy Assessment providing field albedo and diffuse measurements. The typical tower height used in this study is 10 m and then the footprint of the albedo measurements is 127 m (see  Román et al.
PROBA-V data sets The quality assessment is performed against a data set of PROBA-V SA V1 Collection 300 m images covering 15 tiles encompassing a wide European region from 35°to 65°of latitude and from -20°to 30°of longitude. The dataset is available at 10 days frequency covering the whole year 2014. For each tile, files in HDF5 format were considered with the content of black-sky and white-sky albedos in visible, NIR and shortwave domains, plus ancillary information (error estimate, Quality Flag, Z_Age).
Accuracy assessment from EFDC The accuracy assessment of PROBA-V SA Collection 300 m products   20, 2014. 03. 20, 2014. 05. 20, 2014. 07. 20, 2017. 09. 20 and 2014. 11. 20. finally prevails with stations from the European Fluxes Database Cluster (EFDC) (http://gaia. agraria. unitus. it/home/log-in/). These latter are coping with the mandatory criteria aforementioned. Land cover characteristics were obtained at the spatial resolution of 500 m based on Google Earth™ for sites matching first the requirement of homogeneity around the tower flux  (Román et al. , 2009). Both daily and noon measurements were harnessed. Different strategies have been applied to the ground measurements in order to fairly match with satellite data, which depends on the instrument. In case of PROBA-V, the value of the composite period is assigned to the true date.
Missing data are conspicuous for MODIS due to discarding data based on Quality Assurance. The NDVI of Chimbolton (UK) is garbled by cloudiness. But despite two sensors (TERRA and AQUA) against one sensor for PROBA-V, MODIS displays less and more erratic NDVI products. The site of Merguellil (Tunisia) with crops reveals a good correlation between MODIS and PROBA-V (using Z_Age) except at the onset where a bias is noticed. MODIS NDVI is above PROBA-V during winter months. Same conclusion applies for the deciduous forest of Harth (France) and the rice crop of Albufera (Spain). This remains valid for the cropped area of Castellaro (Italy) where PROBA-V NDVI shows at the onset a first vegetation peak not clearly depicted by MODIS C6. It follows shared features for a plateau and the decay.
Therefore, the cross-comparison was limited to data sets ingestion beyond a value of 0. 5 typically. The narrow to broadband conversion process also represents a possible source of future improvement for PROBA-V. Time and space good consistency are noticed between the two sensors, with overall discrepancies (RMSE) of 0. 03 for PAR and shortwave domains, and around 0. 04 for NIR. PROBA-V Collection 300 m displayed reliable temporal trajectories, matching with temporal trend from MODIS C6 and daily ground observations. Smooth transitions may prevail as well as surges in albedo values, to be reasonably reproduced. The accuracy assessment performed over 10 EFDC homogeneous targets shows overall uncertainty (RMSE) of 0. 032 with a mean bias of 0. 01, which is about the same order as MODIS C6. Although this new production presents some spurious variability on short time scales, the comparison against MODIS C6 is deemed quite promising at this stage.
This dataset presents two series of hyperspectral images of healthy and infected apple tree leaves acquired daily, from two days after inoculation until an advanced stage of infection (11 days after inoculation). The hyperspectral images were calibrated by reflection correction and registered to match the geometry of one reference image. On the last experiment day, scab positions are provided. & 2017 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4. 0/).
Value of the Data The data provide a spatial, spectral, and temporal tracking of apple scab disease in a hyperspectral image sequence. Thus, they allow any other researcher to perform chemometric analyses for early disease detection. The images provided were registered so that pixel positions match between dates. The data could be used to test image processing methods for pathogen detection at early or later stages of the infection. The data were acquired using NIR hyperspectral camera and they could be compared to other disease detection measurements  [1]. The data were acquired at leaf-level. Thus, they can be used to establish a link with plant phy- siology studies.
Data Data provided in this article relate to two series of hyperspectral images of healthy and inoculated apple tree leaves acquired daily, from day 2 to day 11 after inoculation using NIR hyperspectral camera. Due to weekend lag, images are lacking on days 7 and 8 after inoculation. Apple scabs become visible to the naked eye at day 9 after inoculation. Eight spots were extracted from both the infected and healthy leaves at day 11 after inoculation. Mean spectrum was calculated for each spot, providing 8 spectra from infected spots and 8 spectra healthy ones. Spectra were preprocessed by applying the logarithm, yielding those presented Fig. 1. Principal Component Analysis PCA was calculated on these spectra using Matlab software R2012b and tested on hyperspectral images at three stages of the infection process (days 11, 06, 02) (Figs.
| Sequence analysis and statistics The assembly of paired-end sequences was performed using QIIME (v. 1. 9. 1)  (Edgar, 2010)  and PANDAseq (v. 1. 0) (Maselle, Bartram, Truszkowski, Brown, & Neufeld, 2012). Only paired sequences between 400 and 500 pb with a minimum overlap of 100 bp were kept for further analysis. Chimeric sequences were then removed using QIIME (Usearch61) to ensure that assembled sequences truly resulted from the same operational taxonomic unit (OTU). OTUs from each sample were assigned to the paired reads using the de_novo method at 97% similarity with the SILVA123 database. An OTU table was then obtained and processed using R (3. 2. 3) and Phyloseq package. A total of 241,016 OTUs was obtained. Before data analysis, OTUs were filtered to remove Unidentified taxa. This step reduced the OTUs number to 212,352.
Identification of main OTUs composing the water and gut microbiota was performed by representing the twenty most abundant OTUs of each environment. OTUs were grouped according to family taxonomic rank and visualized with abundance barplots, using ggplot2 package under R. An additional abundance barplot was generated to allow the visualization of the gut and water microbiota composition according to the phylum taxonomic rank. At last, further analysis of gut microbiota composition was carried out by comparing the top 5 OTUs composing each parrs' group microbiota, represented at the genus level.
After washing, assays were developed using 100ml TMB solution and incubated at RT for color development. Assays were stopped by H 2 SO 4 and ODs were measured at 450nm. Antibody concentration was determined by Softmax Pro software. Antibodies with concentration higher than 5mg/ml were selected to test for polyreactivity with LPS, dsDNA and Insulin by ELISA. In brief, enhanced protein-binding ELISA plates were coated with 50ml of LPS (10mg/ml) or insulin (10mg/ml) or dsDNA (10mg/ml) in carbonate buffer and incubated at 4 C overnight. After washing, plates were incubated with 100ml nonpurified antibodies for 2 hours at 37 C and washed again. Nonpolyreactive (mGO53), low polyreactive (JB40), highly polyreactive (ED38) recombinant human monoclonal antibodies served as controls and were included on each plate.