dataesr/scientific-paragraphs-categorization huggingface dataset:
Data The test area is a mountainous forest in the East of France. 8 areas of 1 km 2 composed of a wide range of tree species are processed (see Figure  13 ). The multispectral images have 4 bands; 430-550 nm (blue), 490-610 nm (green), 600-720 nm (red) and 750-950 nm (near infra-red) at 0. 5 m spatial resolution. The average point density for airborne lidar data is 3 points/m 2. Data was acquired under leaf-on conditions. The lidar data was pre-processed: the point cloud was filtered in order to remove outliers and determine ground points. The ground points were extrapolated so as to derive a Digital Terrain Model (DTM) at 1 m resolution. Then, the DTM was subtracted from the point cloud since a normalized point cloud is necessary in order to perform the coarse tree delineation. The multispectral images and ALS data are perfectly coregistered but were acquired at different epochs.
Some other vegetation indices can also be derived from hyperspectral data. The use of higher density ALS data ( ∼ 10 pts/m 2 ) might also improve the results of the method; trees would be extracted more precisely and some new structural features could be derived. For land-cover mapping, the energetical framework will be modified in order to be able to retrieve other levels of hierarchical forest databases, with the same inputs (trees and species): mixed forests (not any of a single tree specie cover > 75%) and open forests (canopy cover between 10% and 40%). Finally, during the training step of the classifiers, some pixels might not belong to the species of the concerned polygon (since polygons are pure at least at 75%) and only few classes are available. The model should be trained on a larger area and an unsupervised classification should be conducted in order to remove outliers and better tailor the training set.
g. Facebook or MySpace), and, more relevant to the presented work, community contributed photo collections (e. g. Flickr (https://www. flickr. com/) or Panoramio (http://www. panoramio. com/). The advantages of VGI are its temporal coverage, which is often better both in terms of frequency and latency than traditional sources. How-CONTACT Sébastien Lefèvre sebastien. lefevre@irisa. fr ever, they come with a loss in data quality since user inputs are usually made available without review and without metadata (e. g. data source and properties). Georeferenced photo collections are enabling a new form of observational inquiry, which is termed "proximate sensing" by  Leung and Newsam (2010). This concept depicts the act of using ground-level images of close-by objects and scenes rather than images acquired from airborne or satellite sensors.
Study area and data set The study area focuses on several cities in France: Vannes, Rennes, and Nantes in Brittany, and Dijon in Burgundy. For the sake of conciseness, we provide visual illustrations for the Vannes city only, but reported accuracy includes the whole data-set. Experiments on Vannes city focused on the surroundings of the Tohannic Campus which hosts Université Bretagne Sud and IRISA research institute where the authors are affiliated. This choice is motivated by: (i) the availability of ground truth that can be assessed by in situ observations and (ii) the appearance of many new buildings over the last few years (with availability of data acquired both before and after these changes). It covers a 1-km 2 area. The geographical extent is provided in Figure  1. Ground-level images were grabbed from Google Street View (https://www.
Experiments and results We recall that our method was evaluated with preliminary experiments on several cities in France (see Section 2), namely Vannes, Nantes, and Rennes in Brittany, and Dijon in Burgundy. Aerial images have been extracted from Bing Maps. Ground-based imagery have been either downloaded from Google Street View or captured in situ by some volunteers involved in these experiments (for the Vannes site only). Aerial images are dated from 2011 to 2012 while ground-level data were taken either in 2013 (Google Street View) or in 2015 (Google Street View or in situ observations). 100 significant locations were selected for the study site and therefore related ground-level P and aerial A images were included in the experiments. Figure  6  shows the 100 panoramic images used in our study, while Figure  7  shows the 100 corresponding aerial images.
After BAC-FISH metaphases were photographed and the slides were further washed with glacial acetic acid (3:1, v/v), 2xSSC (saline sodium citrate buffer), and increasing ethanol series before hybridization with the rDNA probes according to  Alves et al. (2012). Slides were analyzed with appropriate filters in the epifluorescence microscope Imager Z1 (Zeiss). Images were captured by the monochromatic camera AxioCam Hrm (Zeiss) through the AxioVision software (Zeiss) and assembled by Photoshop CC software.
Karyotype Measurements Chromosomes were paired by FISH marks, AT-rich bands, and the relative position of the primary constriction, from the biggest to the smallest pair. Measurements of total length and arm ratio were made in chromosomes of five metaphases with the measurement module of the AxioVision software. The nomenclature of the chromosomes was according with Levan and colleagues recommendations  (Levan et al. , 1964) : M (centromere at median point), m (centromere at median region), sm (centromere at submedian region), and st (centromere at subterminal region).
Samples were analyzed within a 5 min period in a Partec CyFlow Space flow cytometer (532 nm green solid-state laser, operating at 30 mW; Partec GmbH. , Görlitz, Germany). At least 1300 particles per G1 peak were acquired per samples using the Partec FloMax software v2. 4d (Partec GmbH, Münster, Germany)  (Suda et al. , 2007). Despite of the difficulty of analyzing Eucalyptus species using flow cytometry, the average CV value for the G1 peak was below 5% (mean CV value = 4. 48% for Eucalyptus spp. ; mean CV value for the standard = 3. 12%). The genome size in mass units (2C in pg; sensu  Greilhuber et al. , 2005)  was obtained as follows: Eucalyptus sp. 2C nuclear DNA content (pg) = (Eucalyptus sp. G1 peak mean / reference standard G1 peak mean) * genome size of the reference standard. Differences in genome size among species were evaluated with a One-Way ANOVA (SigmaPlot).
The presence of both genes of interest was confirmed by Blastn against the non-redundant nucleotide database of NCBI. Besides, EGC_Ba_P37H11 and EGC_Ba_P22O03 sequences mapped as expected at the scaffold J of E. grandis genome  (Myburg et al. , 2014) , in the region containing the bona fide EgrCCR1 (Egr. J03114)  (Carocha et al. , 2015)  and the EgrGTPase-RAC (Eucgr. J02468). EGC_Ba_P22O03 and EGC_Ba_P37H11 sequences were deposited at GeneBank under the accession numbers KU727161 and KU727162, respectively. RepeatMasker Web Server (http://www. repeatmasker. org/ cgi-bin/WEBRepeatMasker) vs. open-4. 0. 5 was used to screen both BAC clone sequences against the DNA sequences in FASTA format against the Repbase-derived RepeatMasker library of repetitive elements (RMLib: 20140131) or against the Dfam database (Dfam: 1.
ACKNOWLEDGMENTS We are grateful to  Paulo Forte ,  Paula Paes , and  Paula Soares  for providing the seeds and other plant material. We also thanks of  Victor Carocha  and  Sonia Vautrin  for the technical help on BAC libraries. The authors acknowledge FCT ( Fundação para a Ciência e a Tecnologia ) for supporting this research under the frame work of project " GenEglobwq -Scanning for candidate genes underlying a pulp yield QTL in Eucalyptus globulus " ( PTDC/AGR-GPL/66564/2006 ),  BioResources 4 Sustainability unit (GREEN-IT)  and  FCT LEAF (Linking Landscape, Environment, Agriculture and Food) Unit  ( UID/AGR/04129/2013 ). TR was supported by funding from  FCT  with a  Post-Doc grant  ( SFRH/BPD/64618/2009 ). JP acknowledge his research contract in the frame of EU- FP7-ERAChairs-PillotCAll-2013 project  " Biotalent -The creation of the Department of Integrative Plant Biology " ( FP7-REGPOT-621321 ).
Aims. We present the first near-IR milli-arcsecond-scale image of a post-AGB binary that is surrounded by hot circumbinary dust. Methods. A very rich interferometric data set in six spectral channels was acquired of IRAS08544-4431 with the new RAPID camera on the PIONIER beam combiner at the Very Large Telescope Interferometer (VLTI). A broadband image in the H band was reconstructed by combining the data of all spectral channels using the SPARCO method. Results. We spatially separate all the building blocks of the IRAS08544-4431 system in our milliarcsecond-resolution image. Our dissection reveals a dust sublimation front that is strikingly similar to that expected in early-stage protoplanetary disks, as well as an unexpected flux signal of ∼4% from the secondary star. The energy output from this companion indicates the presence of a compact circum-companion accretion disk, which is likely the origin of the fast outflow detected in Hα.
Acknowledgements. MH and HvW acknowledge support from the  Research Council of the KU Leuven  under grant number  GOA/2013/012. JK acknowledges support from a  Marie Curie Career Integration Grant  ( SH-06192 , PI:  Stefan Kraus ) and the  French   POLCA  project ( ANR-10-BLAN-0511 ). PIO- NIER  is funded by the  Université Joseph Fourier (UJF) , the  Institut de Planétologie et d'Astrophysique de Grenoble (IPAG) , the  Agence Nationale pour la Recherche  ( ANR-06-BLAN-0421 ,  ANR-10-BLAN-0505 ,  ANR-10-LABX56 ,  ANR-11-LABX-13 ), and the  Institut National des Science de l'Univers (INSU PNP  and PNPS). The integrated optics beam combiner is the result of a collaboration between IPAG and CEA-LETI based on CNES R&T funding. This research has made use of the JMMC SearchCal service (available at http://www.
n. , a population of OVA-T cells was found in the third, fourth or fifth division. In agreement with previous observations, no CFSE fluorescence was detected corresponding with T cells in first or second division. Therefore, this population reflects cells that have differentiated in the CLNs and entered the circulation upon exiting the CLNs. Administration of Fp A2-165 together with OVA significantly increased the number of divided OVA-T cells isolated from spleens compared to control mice (Fig. 6a  and Supplementary Fig. S5 ). Together, these data demonstrate that i. n. administration of Fp A2-165 enhances the number of OVA-T cells that divide in the CLNs. In contrast, Ch 82-B administration significantly decreased the proliferation of OVA-T cells isolated from CLNs compared to the control and Fp A2-165 (Fig.
Ex vivo DO11. 10 T-cell restimulation. See Supplementary Methods. Flow cytometry. See Supplementary Methods. Statistics and principal component analysis. Differences in NF-κ B activation in the TLR assays, cytokine secretion, surface marker expression and percentage of dividing or positive cells were analysed comparing samples treated with the bacteria or LPS with the untreated control. Data were analysed by one way Anova followed by Dunnett's multiple comparison test for the in vitro assays or Newman-Keuls multiple comparison test for the in vivo assays using the GraphPad PRISM (GraphPad Software). PCA was used to analyse the variance of the level of cytokines along the different types of bacteria studied. PCA was computed on the standardized data by using the function princomp of the software Matlab.
Acknowledgements This work was financially supported by the  EC   FP7 Cross-talk project  ( PITN-GA-2008-215553 ). The authors thank the Histology Platform from GABI research unit and especially  Abdelhak Boukadiri  for their technical support in the histology sample preparation and  Marlène Héry ,  Charline Pontlevoy ,  Jerome Pottier  and  André Tiffoche  ( UE0907   IERP ,  Jouy en Josas ) for their help during animal experiments. The authors thank  Rafael Muñoz-Tamayo  ( INRA ) for his help in performing the PCA.
Microscopy and FLIM analysis: The transmission and fluorescence images of stained spores were collected on a Nikon C1Si Eclipse TE 2000 U confocal microscope and analyzed using the EZ-C1 software 3. 50 (Nikon, Japan). Imaging was carried out with a ×100 PlanApo objective (NA: 1. 4, oil, Nikon, Japan). An argon laser at 488nm has been used for excitation and emission was collected at 550-700 nm for PI and 500-600 nm for Bodipy-C12. The FLIM experiments were performed as described previously  [23]. Briefly, an aliquot of spore's sample (10 µl) was placed on a microscope coverslip and covered with a pad of 10 % agarose to hold the cells in place and to preserve moisture. The slides were discarded after 30 min of imaging. The FLIM system (LSM kit, Picoquant) was incorporated into the microscope and consisted of a pulsed diode laser (485 nm, FWHM = 83 ps, 40 MHz) and a double SPAD detector.
Images of 256x256 pixels were recorded for about 210 s with a pixel dwell of 9. 60 µs. TCSPC lifetime recording was performed over 200 temporal channels (final resolution of 128 ps/channel). FLIM images were analyzed using TRI2 software version 2. 4. 4. 1 (Gray Institute, Oxford  [36] ). In order to obtain about 1000 counts in the pixel peak maxima, circular binning of 4 was used for analysis of the different wild type spore samples, whereas a circular binning of 2 or 3 was used for cotE gerE spores. We also used a signal threshold between 10-20% and 100% and mask tools to avoid noise and collecting signal from weakly stained internal parts of spores (the spore's core). Wild type spores were analyzed using a bi-exponential fitting (Marquardt algorithm) for each pixel of the decay curves whereas cotE gerE spores were analyzed with a monoexponential fitting.
Viscosity values were obtained from lifetime measurements of Bodipy-C12 using the following equation  [28]  : log  = -0. 75614 + log η *0. 45691 ( 1 ) where τf is the lifetime of Bodipy-C12 in ns and η is viscosity in cP. This expression provides a direct means of converting the lifetime of the Bodipy-C12 into the micro-viscosity of the probe's environment. Statistical analysis have been performed using the software Sigma-plot in order to compare the lifetime values obtained with different perturbations.
Fluorescence lifetime measurements. Following successful staining of ethanol treated spores with Bodipy-C12, we have recorded fluorescence lifetime (FLIM) maps of wild type and cotE gerE spores in order to determine the viscosity of their inner membranes as a function of perturbation with ethanol. Only the deep-stained spores (showing the inner-membrane staining) were considered and analyzed for viscosity, unless otherwise indicated. We have initially considered the viscosity of the membrane within coatless cotE gerE spores. These spores exhibit monoexponential lifetime of Bodipy-C12, that was previously assigned to the inner membrane of the spore  [23] , and hence the data should be straightforward to interpret. Also, a good percentage of deeply permeabilised spores was detected at all ethanol concentrations, from 63% deep staining (at 30% ethanol) to 97% deep staining (at 70% ethanol), Fig.
Conclusions In this work we have used a variety of techniques to investigate the structure of Bacillus subtilis spores following perturbation with ethanol at high temperature. Our combined spectroscopic data on permeability and survival of the spores indicates that high percentages of ethanol (i. e. ≥ 50 %) when used at high temperature lead to a significant permeabilisation of the inner membrane. In order to quantitatively assess the permeability and rigidity of the inner membrane of treated spores we have utilized FLIM microscopy in combination with viscosity-sensitive membrane-bound molecular rotor Bodipy-C12 that was able to provide a measure of microviscosity change in the membrane upon perturbation. Consequently, we have detected a significant decrease in viscosity of the spore's inner membrane, while the outer membrane viscosity appeared unchanged upon perturbation.
Acknowledgements PL thanks the  French Ministry of Research and the Regional Council of Burgundy  for financial support. MKK is thankful to the  UK's Engineering and Physical Sciences Research Council (EPSRC)  for the  Career Acceleration Fellowship  (grant number:  EP/I003983/1 ). We would like to thank  Mr Yilei Wu  for the synthesis of Bodipy-C12. We are grateful to  Barbara Setlow  ( Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, USA ) for providing the PS533 and PS4150 mutant strains. We also wish to thank  Dr P. R Barber  ( Oxford ) for providing access to the TRI2 software.
47 Ab-initio calculations. Ab initio total-energy calculations of arsenolite were performed within the framework of density functional theory (DFT). 48 Vienna Ab initio Simulation Package (VASP) was used to carry out calculations with the pseudopotential method and the projector augmented wave (PAW) scheme, which replace the core electrons, make smoothed pseudovalence wave functions and take into account the full nodal character of the all-electron charge density in the core region. 49 Exchange and correlation term was computed through PBE for solids prescription. 50 Lattice-dynamics calculations at the zone center ( point) of the Brillouin zone were performed using the direct force constant approach. 51 The elastic constants can be obtained by computing the macroscopic stress for a small strain with the use of the stress theorem.
Acknowledgements Financial support from the  Spanish Consolider Ingenio 2010 Program  (Project No. CSD2007-00045 ) is acknowledged. The work was also supported by  Spanish MICCIN  under projects  MAT2014-46649-C4-1/2/3-P  and from  Vicerrectorado de Investigación de la Universitat Politècnica de València  under projects  SP20140701  and  SP20140871. Supercomputer time has been provided by the  Red Española de Supercomputación (RES)  and the MALTA cluster. J. A. S. acknowledges  Juan de la Cierva fellowship program  for his financial support. A. M. and P. R. -H. want to acknowledge to  S. Muñoz Rodríguez  for providing us with a data parsing application. A. L. J. P. acknowledges financial support through  Brazilian CNPq  (Project Nº  201050/2012-9 ).
The amplicons were sequenced using the Big Dye Terminator Cycle Sequencing Kit (Perkin Elmer Applied Biosystems, Foster City, CA) with an ABI automated sequencer (Applied Biosystems). The electropherograms which were obtained were assembled and edited using ChromasPro software (ChromasPro 1. 7, Technelysium Pty Ltd. , Tewantin, Australia) and compared with those available in GenBank database by NCBI BLAST (http://blast. ncbi. nlm. nih. gov/Blast. cgi).
Data analysis For comparison, the head lice DNA sequences obtained in this study were combined with the 30 cytb haplotypes reported by Drali et al. [39]. We then complemented this dataset with newly available sequences in GenBank, then assigned them to haplotypes using DnaSP v5. 10  [40]. Finally, we created a dataset that consisted of 51 haplotypes. These haplotypes span 41 geographic locations (countries) in five continents (S1 Table ). In order to investigate the possible relationships between the haplotypes, the median-joining (MJ) network using the method of Bandelt was constructed with the program NET-WORK4. 6 (www. fluxus-engineering. com/sharenet. htm) [41]. Phylogenetic analyses and tree reconstruction were performed using MEGA software version 6. 06  [42]  with 500 bootstrap replications.
The clade C, representing the most divergent lineage in which two sub-clades can be defined, here referred to as sub-clade C1, which consists of head lice from Ethiopia, France and the Asian continent, and sub-clade C2, which consists of head lice from Senegal and Mali. Sixty-one of these infected lice were from Pokola, forty-one from Thanry-Ipendja, and one hundred and thirty-three from Bene-Gamboma. Molecular identification of Borrelia species. We succeeded in amplifying a 344-bp fragment of the flaB gene from all 11 lice belonging to clade A which were positive in qPCR. The comparison with the GenBank database sequences identified ten (10/11) of the obtained sequences as B. recurrentis with 100% similarity, and the one remaining sequence was identified as B. theileri with 99% identity. The phylogenetic position of these Borrelia is shown in Fig 4.
The sequences of these two Borrelia were deposited in the GenBank under the accession number: KX444533-KX444534. Molecular identification of Acinetobacter species. We succeeded in amplifying a fragment of the rpoB gene in 202 of the 235 samples that were positive in qPCR for Acinetobacter spp. The comparison of the nucleotide sequences with the GenBank database sequences revealed that only 144/202 (71. 3%) sequences match eight species of Acinetobacter sharing 98-100% similarity, which are, in order of decreasing frequency: Acinetobacter junii (37/202; 18. 31%),  Table  4. The other 52/202 (25. 74%) sequences also rated resembled Acinetobacter but were of poor quality, which is assumed to be due to co-infection with several Acinetobacter species. Six of the 202 (2. 97%) remaining sequences revealed 76% identity with the sequence of Moraxella osloensis (accession no.
AP017381). It may represent the DNA of an as yet unisolated and undescribed bacterial species of Pseudomonadales. The phylogenetic tree demonstrated that all Acinetobacter species were classified in the same group as the reference sequence strain and showed that all the Moraxellaceae bacterium were classified in the same group as the Moraxella species but formed a separate branch on the phylogenetic tree (Fig  5 ). The partial rpoB sequences of the Acinetobacter species and the Moraxellaceae species obtained in this study were deposited in the GenBank under the accession number KX444507-KX444532 and KX444535-KX444537, respectively.
The second hypothesis is that, as head lice feed only on human blood  [5] , the acquired infection would be from the blood of patients with ongoing bacteremia. Although, humans infected with this spirochete have not been described in the literature, the transmission of this pathogen to humans may not be ruled out. Moreover, the sequence generated in this study was more similar by flaB sequence comparison to those reported from Ornithodoros sp. soft tick (GenBank KP191621) collected from cave in Israel, than, those reported from Rhipicephalus hard tick (GenBank KF569936) from Mali, as shown in the phylogenetic tree (Fig  4 ). Ornithodoros ticks can feed from multiple warm-blooded vertebrates, including humans, and are known to transmit several species of Borrelia to humans  [27, 43] , thus taking in consideration that the epidemiology of B.
The 150 paired-end sequencing reaction was performed on a MiSeq platform (Illumina) at the Gut Microbiome and Large Animal Biosecurity Laboratories, Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada. The sequencing data were deposited into the Sequence Read Archive (SRA) of NCBI (http://www. ncbi. nlm. nih. gov/sra) and can be accessed via accession number SRR2181770.
Bioinformatic Analyses The PANDAseq assembler  (Masella et al. , 2012)  was used to merge and fix overlapping paired-end Illumina fastq files. All sequences with mismatches or ambiguous calls in the overlapping region were discarded. The output fastq file was analyzed by downstream computational pipelines of the open source software package QIIME  (Caporaso et al. , 2010b). Assembled reads were de-multiplexed according to barcode sequences; those with a read length <175 bases were removed from downstream analysis. Chimeric reads were filtered using UCHIME  (Edgar et al. , 2011)  and sequences were assigned to Operational Taxonomic Units (OTU) using the QIIME implementation of UCLUST  (Edgar, 2010)  at 97% pairwise identity threshold. Taxonomies were assigned to the representative sequence of each OTU using RDP classifier  (Wang et al.