dataesr/scientific-paragraphs-categorization huggingface dataset:
(3) Object-based classification represents a powerful tool to study the ecological requirements of fauna, especially in urban areas. Remote sensing techniques using open-source software such as Orfeo ToolBox may be particularly useful for invasive species management but also for the conservation of native fauna by highlighting ecological preferences regarding their breeding and feeding areas. The Platanus sp. distribution map generated in this study will be used as an environmental predictor for the study of ring-necked parakeet population dynamics through Species Distribution Models (SDMs). One of the major issues of SDMs is to obtain environmental layers which are temporally coherent with the occurrence data of the target species. In our opinion, remote sensing is one of the most powerful and time/cost-friendly techniques which will enable the generation of spatio-temporally consistent species distribution models (SDMs) called by He et al.
III. DATA MEG and EEG were measured using 306 system (102 magnetometers, 204 planar gradiometers), and 70 EEG channels recorded EEG data simultaneously. Stimuli were presented in six 7. 5 min runs. The face stimuli contain two sets of 300 gray scale photographs, half from unfamiliar people (unknown to the participants) and the remaining from famous people. In a third condition, 150 photographs of scrambled faces are obtained from either famous or unfamiliar people. The reader is referred to  [9]  for more details. In this work, we are interested in localizing face recognition areas. For this reason, we use only the measurement acquired when using photos of famous people subtracted to the ones obtained when using scrambled faces. Low pass filter of cut-off frequency 35 Hz was used to smooth the data.
The remaining two are affected by the choice of (α, β). The results are less dispersed when (α, β) = (  1 2 , 1 2 ) (see left side of Fig (  1c )). B. Real data iSDR(p=2) is applied to MEG data of 9 subjects from  [9]. In  [12] , the authors show that subjects may have right or bilateral fusiform gyrus (FF) activation if they are right or left handed, respectively. In Several works  [9, 4]  show that activation in the FF between 170 and 200 ms is observed when performing face recognition task which coincides with what we observe in this work. In the majority of subjects, regions in the superior posterior temporal lobe, medial parietal, temporal pole (TP), orbitofrontal (OF) are found to be active. This coincides with the findings of other works with the same dataset  [9, 4]. We have found interactions between TP and frontal lobe (FL), left and right FL, inferior occipital and temporal gyrus with OF.
The primary antibodies used were: chicken anti-MAP2 (1/10000, Abcam), mouse anti-ankyrinG (1/100, NeuroMab N106/36, IgG2a), mouse anti-Kv1. 1 (extracellular epitope, 1/100, NeuroMab K36/15, IgG2b) and mouse anti-Kv1. 2 (1/100, NeuroMab K14/16, IgG2b). The secondary antibodies used were goat anti-mouse IgG2a-Alexa-Fluor-594, IgG2b-Alexa-Fluor-488 and anti-chicken-Alexa-Fluor-647 (1/1000). Images were acquired in a Leica TCS SP5 laser scanning microscope (Leica Microsystem). Electrophysiological recordings and data analysis. CA3 pyramidal neurons were whole-cell recorded in organotypic cultures. The external solution contained (mM): 125 NaCl, 26 NaHCO 3 , 3 CaCl 2 , 2. 5 KCl, 2 MgCl 2 , 0. 8 NaH 2 PO 4 and 10 D-glucose, and was equilibrated with 95% O 2 -5% CO 2. Patch pipettes (5-10 MΩ) were filled with a solution containing (in mM): K-gluconate 120; KCl 20; HEPES 10; EGTA 0.
5; MgCl 2 2; Na 2 ATP 2; NaGTP 0. 3 (pH 7. 4). All recordings were made at 29 °C in a temperature-controlled recording chamber (Luigs & Neumann, Ratingen, Germany). Neurons were recorded in current clamp with a Multiclamp 700B amplifier (Axon Instruments, Molecular Devices) and were held at resting membrane potential (~-65 mV). The effect of the D-current was monitored by injecting a long (1 s) depolarizing current pulse. The voltage and current signals were low-pass filtered (3 kHz), and acquisition was performed at 10 kHz with pClamp10 (Axon Instruments). Access resistance and capacitance were checked by injecting a small hyperpolarizing current. Data were analyzed with ClampFit (Axon Instruments) or self-developed software written in Labview (National Instrument). Pooled data are presented as mean ± SE and statistical analysis was performed using the Mann-Whitney U-test or Wilcoxon rank-signed test.
Acknowledgements We thank  Laure Fronzaroli-Molinieres  for help with the cultures. Supported by  Institut National de la Santé Et de la Recherche Médicale (INSERM) ,  Centre National de la Recherche Scientifique (CNRS) ,  Ministère de l'Enseignement Supérieur et de la Recherche ,  Fondation pour la Recherche Médicale  (grant  FDT20150532147 ),  Agence Nationale de la Recherche  (grants  ANR-11-BSV4-016-01 & ANR-14-CE13-003 ) &  Spanish Ministry of Economy and Competitiveness (MINECO ,  SAF2015-65315-R ).
Strain identification and phylogenetic analysis The analysed samples were collected and stored at -80°C. Eighteen standard culture conditions were tested on the samples under variable conditions in a dilution series ranging from 1/10 to 1/10 10 to isolate these strains, as previously described  [13]. The samples' origin and conditions of isolation are summarized in Table  1. Blood culture bottles were monitored 1 month after inoculation. According to the manufacturer's recommendations, identification of isolated colonies was performed using a Microflex LT  spectrometer (Bruker Daltonics, Bremen, Germany) and a MSP 96 MALDI-TOF MS target plate (Bruker Daltonics), as previously described  [15]. The obtained spectra were imported into MALDI Biotyper 3. 0 software (Bruker) and were compared with the computer databases at the Bruker base and the basespecific laboratory at the hospital of La Timone, Marseille, France.
We previously updated our database with the spectra of the new bacterial species cultured during our previous study. The resulting score allowed us to identify (or not) the tested species: samples were labeled as correctly identified at the species level with a score of 2; they permitted identification at the genus level with a score of 1. 7 but <2; and samples provided no identification with a score of <1. 7. No significant score was obtained for our strains, thus suggesting that our isolated species were not members of a known species. Consequently, identification of these strains was realized by 16S rRNA gene amplification and sequencing. For nucleotide sequence analyses, DNA was previously extracted by EZ1 DNA Tissue Kit using BioRobot EZ1 Advanced XL (Qiagen, Courtaboeuf, France). The 16S rRNAgene was amplified by PCR by using universal primers pair fD1 and rP2 (Eurogentec, Angers, France).
Sequencing was then realized by using the Big Dye Terminator v1. 1 Cycle Sequencing Kit and ABI Prism 3130xl Genetic Analyzer capillary sequencer (Applied Biosystems, Foster City, CA, USA)  [16]. The obtained sequences were assembled and corrected by CodonCode Aligner software (http://www. codoncode. com) and were compared with the sequences available in the GenBank database by BLASTn (http://blast. ncbi. nlm. nih. gov. gate1. inist. fr/Blast. cgi). A similarity threshold of <98. 7% allowed identification at the species level (new species), whereas a threshold of <95% allowed identification at the genus level (new genus)  [19]. All species from the same family of the new species were automatically retrieved by using a custom Python script, which was able to download 16S rRNA gene sequences from the National Center for Biotechnology Information (NCBI), then separate 16S rRNA gene sequences in two groups: group A, containing the sequences of strains from the same genus, and group B, containing the rest.
It Major cellular fatty acid 15:0 anteiso 15:0 anteiso 15:0 anteiso NA 15:0 anteiso 15:0 anteiso 15:0 anteiso 15:0 anteiso Production of: Alkaline phosphatase All the spectra have been integrated to the URMITE database (http://www. mediterranee-infection. com/article. php? laref=256&titre=urms-database). The comparison of their proteomic profiles was made between our strains and their closest species. - NA - NA - NA + + Catalase + + + + - + + + Oxidase - - - + - - - + Nitrate reductase - + - + - + - + Urease - NA - NA - NA - NA β-Galactosidase + NA + + + NA + + N-Acetyl- glucosamine - NA - NA - - - + Acid from: L-Arabinose + NA + + + - + + Ribose NA NA NA + NA NA NA NA Mannose - NA - + - + - + Mannitol - + - + - + - + D-.
The library profile was visualized on a High Sensitivity Bioanalyzer LabChip (Agilent Technologies), and the final concentration library was measured. Open reading frames (ORFs) were predicted using Prodigal with default parameters (excluding the spanned sequencing gap region)  [27]. The predicted bacterial protein sequences were searched against the GenBank  [28]  and the Clusters of Orthologous Groups database (COGs) databases using BLASTP (E value 1e-03, coverage 0. 7 and identity percent 30%). On the contrary, if no hit was found, it was searched against the NR database using BLASTP with an E value of 1e-03 with a sequence size larger than 80 aa or an E value of 1e-05 if the sequence length was smaller than 80 aa; coverage of 0. 7 and identity percentage was 30%. The RNAmmer tool  [29]  was used to find ribosomal RNAs, while tRNA genes were found using tRNAScanSE  [30].
Closest species were identified in the 16S RNA gene sequence tree using Phylopattern software  [37]  for genomic comparison. At that point, the complete genome sequence, proteome genome sequence and Orfeome genome sequence of each selected genome were retrieved from the NCBI FTP site. Then an annotation of the entire proteome was performed to determine the distribution of functional classes of predicted genes according to the COGs of proteins (same method as for the genome annotation). Annotation and comparison processes were performed by the Multi-Agent software system DAG-OBAH including Figenix libraries to provide pipeline analysis  [38, 39]. Finally, to evaluate the genomic similarity between studied genomes, two main parameters, digital DNA-DNA hybridization (dDDH)-which exhibits a high correlation with DDH-and average genomic identity of orthologous gene sequences (AGIOS), were determined  [19, 40].
The major fatty acid is 12-methyltetradecanoic acid. The genome of strain Marseille-P3071 T is 5 823 754 bp long with 47. 45% G+C content. The 16S rRNA gene and genome sequences are available in the European Molecular Biology Laboratory/European Bioinformatics Institute (EMBL/EBI) database under accession numbers LT598550 and FTLT00000000, respectively. The type strain Marseille-P3071 T (= CSUR P3071 = DSM 103972) was isolated from the stool sample of a Senegalese girl with severe acute malnutrition (marasmus form). Its habitat is the human gut. Strain Marseille-P3071 T is the type strain of the new species 'Paenibacillus bouchesdurhonensis' (bou. ches. du. rho. nen'sis, NL. adj. masc. , to refer to Bouches-du-Rhône, the name of the French department where the strain was isolated). Description of 'Paenibacillus rubinfantis' sp.
The major fatty acid is 12-methyl-tetradecanoic acid. The genome of strain MT18 T is 5 370 472 bp long with 53% G+C content. The 16S rRNA gene and genome sequences are available in the EMBL/EBI database under accession numbers LN881603 and FAUQ00000000, respectively. The type strain MT18 T (= CSUR P2076 = DSM 101191) was isolated from the stool sample of a Nigerian child with severe acute malnutrition (kwashiorkor form). Its habitat is the human gut. Strain MT18 T is the type strain of the new species 'Paenibacillus rubinfantis' (rubinfantis is composed of 'ru. bi' (L. adj. neut. ), for rubeus (adj. ), meaning 'red,' and 'in. fan. tis' (L. adj. neut. ), meaning 'infant,' which is a reference to the hair discolouration observed in children with kwashiorkor). Description of 'Paenibacillus senegalimassiliensis' sp.
The major fatty acid is 12-methyl-tetradecanoic acid. The genome of strain SIT18 T is 5 059 702 bp long with 49. 20% G+C content. The 16S rRNA and genome sequences are available in the EMBL/EBI database under accession numbers LN890284 and FAUP00000000, respectively. The type strain SIT18 T (= CSUR P2144 = CCUG 69869) was isolated from the stool sample of a healthy Senegalese boy. It habitat is the human gut. Strain SIT18 T is the type strain of the new species 'Paenibacillus senegalimassiliensis' ('senegalimassiliensis' is composed of 'se. ne. ga. li' (L. masc. adj. ), referring to the Republic of Senegal, the West African country where the stool sample was retrieved, and Description of 'Paenibacillus tuaregi' sp. nov. Cells of the strain Marseille-P2472 T are Gram-variable bacilli and are rod shaped with a length varying from 3.
10% G+C content. The 16S rRNA and genome sequences are available in the EMBL/EBI database under accession numbers LT223571 and FLKE00000000, respectively. The type strain Marseille-P2472 T (= CSUR P2472 = DSM 102801) was isolated from the stool sample of a healthy Nigerian girl. Its habitat is the human gut. Strain Marseille-P2472 T is the type strain of the new species 'Paenibacillus tuaregi' ('tuaregi' from 'tua. re. gi,' L. masc. adj. , tuaregi from 'Touareg,' the people of the sample donor from which the strain was isolated).
45 28 47 155 53. 0 2 488 213 49. 2 2 783 054 49. 1 Coding region (bp) 5 050 020 86. 7 4 689 593 87. 3 4 509 792 89. 1 4 872 040 85. 9 Total genes 5213 100 4983 100 4736 100 5169 100 Protein-coding genes 5113 98. 1 4901 98. 4 4655 98. 3 5061 97. 9 RNA genes 100 1. 9 82 1. 6 81 1. 7 108 2. 1 Proteins with function prediction 3507 68. 6 3523 71. 9 3194 68. 6 3574 70. 6 Proteins assigned to COGs 2198 43. 0 3025 61. 7 2828 60. 8 3040 60. 1 Proteins with peptide signals 670 13. 1 688 14. 0 638 13. 7 703 13. 9 No. of protein associated to ORFan 237 4. 6 122 2. 5 164 3. 5 216 4. 3 Genes with transmembrane helices 1215 23. 8 12. 1 24. 5 1126 24. 2 1255 24. 8 Genes associated with PKS or NRPS 12 0. 2 8 0. 2 13 0. 3 24 0. 5 No. of antibiotic resistance genes 0 0 3 0. 1 0 0 0 0 No. of genes associated with Pfam-A domains 4590 88 4522 90 4240 89 4624 89 COGs, Clusters of Orthologous Groups database; NRPS, nonribosomal peptide synthase; PKS, polyketide synthase.
Evaluation on the Processing Time We evaluated the processing time of the road surface segmentation with the road profile estimation on a PC (Intel Xeon 2. 8GHz) and on a general embedded system (ARM CPU with/without FPGA). The time was measured from the time of the disparity image output to the time of the road profile estimation output. The disparity image computation is performed in a separated image processing hardware which outputs the disparity data line by line. The conventional method is implemented in software, and the proposed method is implemented in 2 ways, one in software, and one in FPGA. For the software implementation of both methods, it is noted that we did not optimize the codes for high speed processing. We coded the both algorithms in Matlab script, and used the C codes generated by Matlab auto code function for the evaluation.
Acknowledgments This study is part of the  EC2CO-Lefe project  " ForChlo " funded by the  CNRS. This study is also strongly supported by the  Region Pays de la Loire  ( Post-doc position of the first author on "COSELMAR" and "Fresco " projects). The authors would also like to thank  Sophie Quinchard  and  Eric Beneteau  from the  LPG-BIAF  for their help at peaking thousands of foraminifera.
This study is part of the  EC2CO-Lefe project  " ForChlo ," funded by the  CNRS  (http:// www. insu. cnrs. fr/ec2coand http://www. insu. cnrs. fr/lefe). This study is also strongly supported by the  Region Pays de la Loire  (Post-doc position of the first author, TJ, on " COSELMAR" and "Fresco " projects). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Furthermore, we performed quantitative and qualitative analysis of phenolics in flax shives using ultra-performance liquid chromatography (UPLC) with a diode and mass detector. The comparison of the quantitative analysis of free phenolic compounds revealed the highest amounts for methanol extraction. Vanillin level (the most abundant compound in flax shives) reached 9. 06 g/g in the water extract and 6. 36 g/g in the methanol extract and was the lowest, 1. 27 g/g, in ethyl acetate. The release of phenolic compounds by alkaline hydrolysis increased their level and was elevated 20-fold for vanillin (224. 46 g/g). All identified metabolites are presented in Supplementary Data Table  1. So far, mainly lignin, cellulose and hemicelluloses have been characterized in flax shives, but also other phenolic compounds are described  [23, 24] , and these have also been identified in the M50 flax type.
Optimization of Alkaline Hydrolysis Conditions. The previous experiments showed that alkali hydrolysis with sodium hydroxide results in a higher yield of phenolic compound extraction from flax shives. In order to optimize the alkaline hydrolysis conditions, the effects of temperature of hydrolysis, sodium hydroxide concentration, and duration of hydrolysis were examined. Firstly, the effect of temperature on release of phenolic compounds from the cell wall was studied. The literature data concerning hydrolysis temperature differ; therefore room temperature, 37 ∘ C, and 65 ∘ C were tested. The UPLC quantitative analysis of identified phenylpropanoids is presented in Table  1. These results suggest that the extraction yields of phenolic compounds are very much temperature specific. The increase of temperature of hydrolysis to 65 ∘ C resulted in the nearly three times higher yield of phenylpropanoids (533.
However, after 48 h of treatment no preparation exhibited any negative effect, and the viability of NHDF cells reached 94. 1% to 122,1%. The highest viability was observed for shives #3 and #4 preparation and reached 122,1% and 114,3%, respectively (Figure  4(b) ). Moreover, flax shives extracts exhibited no cytotoxicity on human fibroblasts. The viable cells, as compared to untreated cells, comprised 92. 4% to 103. 5% after 24 h of incubation (Supplementary Data Figure  2(A) ). Similarly, following treatment of fibroblasts with the flax shives extract for 48 h resulted in cell viability of 95. 3%-105. 7% (Supplementary Data Figure  2(B) ). Furthermore the fibroblasts morphology and nuclei observations were performed. The NHDF cells The NHDF cells treated with flax shives extract #6, with the highest concentrations of phenolics, did not exhibit the typical fibroblast morphology, and altered and impaired phenotype was observed.
5 min. For each time point, six replicates were analyzed and the amount of ET was calculated from the data recorded and analyzed with the MassLynx Waters software by constructing a standard ET curve. For JA quantification, 250 mg of frozen tissue from the third and fourth tomato leaves were added to 80% methanol-1% acetic acid that contained the internal standard dihydrojasmonate (OlChemIm, Czechia), and were mixed by shaking for 1 h at 4 • C. The extract was kept at -20 • C overnight and was then centrifuged. The supernatant was dried in a vacuum evaporator. The dry residue was dissolved in 1% acetic acid and passed through a reverse phase Oasis HLB column  (Seo et al. , 2011). The dried eluate was dissolved in 5% acetonitrile-1% acetic acid, and the hormone was identified using a reverse phase Ultra Performance Liquid Chromatography (UPLC) system coupled to a Q-Exactive mass spectrometer (Orbitrap detector; Thermo Fisher Scientific) by targeted Selected Ion Monitoring (SIM).
Separation was performed in a 2. 6 µm Accucore RP-MS column, 50 mm long × 2. 1 mm i. d. ; (Thermo Fisher Scientific) using a 5-50% acetonitrile gradient that contained 0. 05% acetic acid as the solvent system at 400 µL/min for 14 min. The JA concentration in the extracts was determined using embedded calibration curves with the authentic standard (OlChemIm, Czechia) and the Xcalibur 2. 2 SP1 build 48 and TraceFinder software.
The chromatographic separation of compounds was performed in an Agilent 6890N gas chromatograph (Santa Clara, CA, United States) equipped with a DB-5 ms fused silica capillary column (60 m long, 0. 25 mm i. d. , 1 µm film thickness). The oven temperature conditions were 40 • C for 2 min, 5 • C/min ramp until 250 • C and then held isothermally at 250 • C for 5 min. Helium was used as the carrier gas at 1. 2 mL/min at a constant flow. Detection was performed in an Agilent 5975B mass spectrometer (Santa Clara, CA, United States), which operated in the EI mode (ionization energy, 70 eV; source temperature 230 • C). Data acquisition was performed in the scan mode (m/z range 35-250; six scans per second). Chromatograms and mass spectra were recorded and processed by the Enhanced ChemStation software (Agilent).
Quantitative PCR was carried out as previously described  (Campos et al. , 2014). A housekeeping gene transcript, Elongation Factor 1 alpha (eEF1α), was used as the endogenous reference. The PCR primers were designed using the pcr Efficiency software  (Mallona et al. , 2011)  and are listed in Supplementary Table  S1. The primers used to amplify TomLOXF have been previously described  (Shen et al. , 2014).
Statistical Analysis The statistical analyses of the signal compounds levels (GA, SA, ET, and JA) and the qRT-PCR of the selected genes were done by an analysis of variance (multifactor ANOVA) using Statgraphics Centurion XVI. For the untargeted analysis of the volatile profile, the GC-MS data were processed with the MetAlign software (Wageningen, Netherlands) for the alignment of the chromatograms and the quantitation of each MS feature. The resulting dataset was submitted to a Partial Least Square (PLS) study by the SIMCA-P software (v. 11. 0, Umetrics, Umeå, Sweden) using unit variance (UV) scaling. For the Hierarchical Cluster Analysis (HCA), the ratios for each VOC were calculated and log 2 -transformed for normalization. HCA was performed with the Acuity 4. 0 software (Axon Instruments) with the distance metrics based on the Pearson correlation.
ACKNOWLEDGMENTS We would like to thank  Dr. Selena Giménez-Sánchez  ( Centro Nacional de Biotecnología, Madrid ) for kindly providing us with both strains of Pseudomonas syringae pv. tomato DC3000. We thank  Dr. Isabel López-Díaz  and  Dr. Esther Carrera  for the hormone quantification carried out at the  Plant Hormone Quantification Service, IBMCP, Valencia, Spain. We are also very grateful to  Teresa Caballero  and  Ana Ruiz  for their excellent technical support.
Although genetically very close to PbA  (Otto et al, 2014) , several variants of Pb causing different pathophysiological outcomes have been described (de Souza et al, 2010). Pb K173 (PbK) being the most "distant" from PbA (although SNPs were found only in 469 of > 15,000 genes;  Otto et al, 2014) , we decided to perform this analysis both with PbA and PbK pRBC. This led to the identification of a total of 372 unique I-A b -eluted peptides, comprising 330 mouse sequences and 42 Pb sequences (Fig 1C, Dataset EV1), derived from 13 putative Pb antigenic proteins (Dataset EV2). In line with the modest level of polymorphisms between PbA and PbK, none of those source antigens was polymorphic. Remarkably, for seven antigens, we recovered multiple peptides containing a core of 11-16 amino acids (aa) and various N-or C-terminal extensions (Dataset EV2).