dataesr/scientific-paragraphs-categorization huggingface dataset:
The column packing was a poly (hydroxymethacrylate) gel. The MALLS photometer, a DAWN HELEOS II from Wyatt Technology Inc. (Santa Barbara, CA, USA) was provided with a fused silica cell and a Ga-As laser (λ = 665. 8 nm). The viscometer was a ViscoStar II from Wyatt Technology Inc. (Santa Barbara, CA, USA). The whole collected data: light scattering (LS), dRI and viscosity were analyzed using the Astra v6. 0. 6 software package. Molar mass were obtained with the Zimm order 1 method using angles between 53. 1° and 140°. The concentration of each eluted fraction was determined with dRI (RID10A Shimadzu, Kyoto, Japan) according to the measured values of   ⁄ (0. 144 mL/g). The determination of the average intrinsic viscosity allowed us to obtain the average hydrodynamic volume (Vh, i. e. , the average hydrodynamic radius Rh) using the Einstein-Simha equation: 𝑉 ℎ = []•𝑀 •𝑁 𝐴 where NA is Avogadro's number, M is the molar mass, [η] is the intrinsic viscosity (g/mL), and ν is a conformational parameter that takes the value of 2.
Infrared Spectra Infrared spectra were acquired between 400 and 4000 cm -1 with an AVATAR 370 FT-IR spectrometer (Thermo-Nicolet, Villebon, France) with 32 scans/sample and a resolution of 2 cm -1. Dry samples were pressed with potassium bromide (2% w/w). Spectra were processed and analyzed with OMNIC v6. 1 (Thermo-Nicolet software).
Nuclear Magnetic Resonance (NMR) All NMR experiments were conducted on a Bruker AVANCE III spectrometer (BioSpin Bruker, Wissembourg, France) operating at a proton frequency of 500 MHz with a 5 mm gradient indirect detection probe, at a probe temperature of 300 K. The samples were exchanged twice with 99. 8% D2O with intermediate freeze drying and dissolved in 0. 6 mL of 99. 96% D2O. 1-D proton spectra were acquired with 16 scans and 32 K data points with a spectral width of 5000 Hz. Typical 1 H 9. 5 µs-pulse length and relaxation delay of 1 s were used. Water signal was suppressed by a presaturation sequence at the water signal frequency.
Acquisition and Reconstruction Parameters Imaging was performed 2 h after intravenous injection of radiolabeled fucoidans. Helical SPECT/CT scans were performed under isoflurane anesthesia using a 4-headed multiplexing multipinhole camera (NanoSPECT/CT plus, Bioscan Inc. , Washington, DC, USA). Each head was equipped with a tungsten collimator (Rat Whole Body-High sensitivity). Flat-panel detector CT was performed first (tube voltage: 55 kV, tube current: 145 mAs), then whole body SPECT acquisition was performed with the following parameters: helical scan with 28 projections/rotation plus circular scan at the beginning and at the end of the scan range, matrix size: 256 × 256, zoom: 1. 14 (pixel size: 1 mm 2 ). SPECT data were reconstructed using the HiSPECT (Bioscan Inc. , Washington, DC, USA) iterative reconstruction software on a dedicated workstation, and visualized using InVivoScope software with co-registration of SPECT and CT images.
Data Analysis Radiolabeled fucoidan biodistribution in healthy rats was carried out in order to establish evidence of the preferential route of blood clearance after intravenous injection. Total body activity was estimated using a volume of interest encompassing the whole field of view, subtracted from residual activity remaining at the injection site (penis). Then, relative organ retention (defined for liver, spleen, left kidney, and bladder) was calculated as the ratio of activity within 3-dimensional volumes of interest over total body activity. Results were then displayed as renal excretion (kidney × 2 + bladder) and reticulo-endothelial retention (liver + spleen). Ischemia-reperfusion model scintigrams were assessed visually to determine the presence of a focal tracer uptake in the myocardium.
Acknowledgments This study was supported by  Inserm ,  University Paris 13  and the competitiveness cluster  Medicen Paris Region. P. S. is a recipient of the grant from  University   Paris 13  and  IMOVA  project founded by  FUI/OSEO. The authors would like to thank  Thomas Cognet  and  Fadwa Aï t-Ali  for their technical assistance,  Algues & Mer  for the supplying of fucoidan, and  Richard Bayles  for editing of the manuscript. We also acknowledge the financial supports from  FP7 NMP-LA-2012-309820  " NanoAthero ",  ANR-13-LAB1-0005-01  " FucoChem " and  ANR-13-RPIB-0006  "FucoThrombo".
Acknowledgements This study was supported by the  CRDF Global  Grant  N°TNB1-31117-TU-13 , the  Pasteur Institute of Tunis, Tunis, Tunisia , and the  Institute of Research for Development, Marseille, France. The research leading to these results has received funding from the  European Union 's  Seventh Framework Programme  for research, technological development and demonstration under Grant Agreement numbers 261504-EDENext- FP7  (http://www. edenext. eu)and  FP7   CAPACITIES  project  GA no228292-EVA  (European Virus Archive, http://www. european-virus-archive. com/). This article is catalogued by the EDENext Steering Committee as EDENext# 266. The work of RNC was done under the frame of EurNegVec COST Action TD1303.
We report here the results of the antiprotozoal (against Plasmodium falciparum, Trypanosoma brucei, Leishmania donovani) and fungicidal (against Candida albicans, Candida glabrata and Candida parapsilosis) assays of two crude extracts and six fractions from the stem bark of M. richardiana. Their cytotoxicity was also evaluated on KB, Vero and MRC5 cells. These M. richardiana biological data led to bio-phytochemical correlation between active principles and pharmacological results.
Acknowledgements This work has been carried out thanks to a multidisciplinary and multinational collaboration involving the teams from  CERMA (Congo) ,  CNARP (Madagascar) ,  CNRS  ( Toulouse and Châtenay-Malabry, France ) and with the material, technical and financial support of the  ICSN-CNRS of Gif-sur-Yvette (France ). The authors particularly wish to thank  Jean-Yves Lallemand  ( ICSN-CNRS, Gif-sur-Yvette, France ) who has supported this project. Mrs Geneviève Aubert of the Institut de Chimie des Substances Naturelles  ( CNRS, Gif-sur-Yvette, France ) for the cytotoxicity assays,  M. D. Linas  ( Parasitology-Mycology Dept, Toulouse Hospital ) for the gift of Candida strains,  John Woodley  for editing the English, and all the members of  Médecins d'Afrique  who participated in this work (particularly  Ms Aline Prost ) are also acknowledged.
8% of these genes being immunity-related ones. Forty of the total genes belonging to the HLA system encode leukocyte antigens. The role of these cell-surface antigens is to present pathogen-derived antigens to T cells and to initiate acquired immune responses  [35]. Some of these genes (i. e. , class I and class II genes) are among the most polymorphic in humans. For example, more than 100 allelic variants have been identified in human populations at the HLA-B and HLA-DRB1 loci (IMGT/HLA database,  [36] ). Many associations between alleles or combinations of alleles and susceptibility to infectious and autoimmune diseases have been described in humans e. g. ,  [4, 37]. For HFRS and HCPS, risk HLA haplotypes have been identified according to the following clinical and laboratory parameters of disease severity: treatment time at hospital (overall severity), weight change during hospital care (amount of fluid retention during oliguric phase), need of dialysis, lowest systolic blood pressure, presence of shock, increase of plasma creatinine and urea (severity of acute kidney injury-AKI), decrease of platelets (thrombocytopenia) and increase in blood leukocyte count (leukocytosis)  [19].
These results have nevertheless to be taken carefully as such evidence of lesions remain rare compared to the large number of experimentally infected rodents which did not show any sign of pathology. Kallio et al. [31]  exposed naive bank voles, Myodes glareolus, to beddings previously contaminated by PUUV. They showed that infection outcomes were highly variable among recipient voles, independently of sex or age. Guivier et al. [94]  evaluated whether immunity-related gene polymorphism could explain these differences. Unfortunately, no significant associations could be detected between infection success and immunity-related gene polymorphism of these bank voles. Dqa Mhc class II gene was monoallelic among the 101 bank voles analyzed from this experimental dataset. The relative risk associated with Mygl-Drb*117 was high (RR = 4.
The distribution of Drb Mhc class II gene polymorphism should therefore not be simply used to infer the chance of PUUV infection in bank voles. Genotype-phenotype associations were examined in large European datasets (about 200 bank voles, 65 PUUV-seropositive ones) that included bank voles sampled in Fennoscandia (Finland and Sweden), and in French and Belgian (the Ardennes and the Jura) PUUV-endemic areas. Dqa gene polymorphism did not influence the probability of bank voles being infected with PUUV in most of geographic localities considered  [94]. However, in the French Jura (corresponding to a recently identified area of PUUV endemicity), significant negative associations were detected between the presence of anti-PUUV antibodies and both Cgl-DQA-05 and Cgl-DQA-12 alleles (RR = 0. 21 and 0.
Concluding Remarks In summary, this review aimed at highlighting a number of important immunity-related genes that seem to be associated with the clinical course of hantaviral disease in humans, and the susceptibility of humans and rodents to hantaviruses. Beyond this list, we wanted to emphasize the necessity, in the very near future, to -infect‖ the classical human immunogenetics approach both with evolutionary biology and with the datasets produced by the human genome projects. This combination of approaches, the future accumulation of genetic data using new generation sequencing technologies and genome-wide association studies, as well as closer collaborations between researches developed on wild reservoirs and humans, should ultimately improve our knowledge of hantavirus risk and epidemiology.
Acknowledgments The authors original studies have been partly supported by the European programs GOCE-CT-2003-010284 EDEN and  FP7-261504 EDENext , and the paper is catalogued by the EDENext Steering Committee as EDENext191 (http://www. edenext. eu). Other supports for this work include grants from The  Academy of Finland ;  Sigrid Jusé  lius Foundation;  Helsinki University Hospital, Hospital district of Helsinki and Uusimaa  ( TYH-2011305 ) Research Funds; The  Competitive State Research Funding of the Expert Responsibility Area of Tampere University Hospital; Tampere Tuberculosis Foundation ;  Health/National Institute of Allergy and Infectious Diseases (NIH/NIAD ,  U19 AI57319 ),  INRA-EFPA  projets innovants. MP is currently funded by an  FRS-FNRS fellowship (Belgian Fund for Scientific Research).
In the study presented here, 24-day-old Medicago plants grown in soil were subjected to progressive long-term drought and rewatering treatments in order to mimic what plants experience in their natural environment. Changes in gene transcript and metabolite levels were measured at multiple time points during drought stress, over a 15-day period. We present a comprehensive and detailed overview of the transcriptome and metabolome changes associated with the progression of drought stress, tightly linking our data with physiological measurements of the plant water status during the timecourse of drought progression. This will enable future comparative analysis (i. e. between different germplasm and/or multiple stress combinations). Our goal was also to provide candidate genes that might prove useful in translational approaches for legume crop improvement.
Physiological measuring to one set of plants and taking tissue samples for RNA isolation and metabolite analysis to another set of plants were performed simultaneously at the mimic mid-day time period (1300-1500 h). Leaf water potential (Ψw), relative leaf water content (%) of the up-most fully expanded leaves and the absolute water holding in pots (gram/pot) or percentage of the maximum field capacity have been used to monitor the drought-stress intensity in the preliminary experiments and the final design, although only Ψw will be showed here. The soil mixture used in this experiment made the water loss very gradual until 2 d after watering was ceased (data not shown). Ψw was measured using a thermocouple psychrometer (HR-33T Dew Point Microvoltmeter, and the small sample chambers from Wescor, Logan, UT, USA) and calculated MPa as: Ψ = ΔV/-7.
S1  & S2). Based on these results and other physiological measurement, shoot (S) and root (R) RNA samples of three independent biological replicates of selected drought-stress treatment at day 2, 3, 4, 7, 10, 14 (named as D2/3/4/7/10/14D-S/R, respectively), 24 h post-rewatering of the 14-day drought-stressed plants (named as D14RW-S/R, respectively), and two wellwatered controls at day 2 and day 4 (equalling to 26-or 28-day-old plants, named as D2W-S/R and D4W-S/R, respectively) were analysed. Data extraction and normalization was performed as previous described  (Benedito et al. 2008).
Compound derivative identification and quantification were conducted using the Metabolomics Ion-based Data Extraction Algorithm (MET-IDEA) developed and described by  Broeckling et al. (2006). Due to visible chromatography difference, shoot and root samples were analysed separately. Triplicate biological samples were used for the assay. Chromatography peaks presenting in all three replicates were extracted and quantified by selected single ions of the mass spectrums, with known or unknown derivatives/compounds/ pools described as m/z of the selected ion, retention time of the compound (min) and identifier. The relative abundance of each derivatives/compounds/pool was normalized to the internal standards. Principal component analysis (PCA) was performed on Log10 transformed dataset of the mean values with Spotfire (TIBCO, Somerville, MA, USA) software.
Metabolome analysis of drought-stressed Medicago plants To detect drought stress-associated metabolites in shoots and roots of Medicago and to examine their accumulation/ degradation trends during the progression of drought stress and recovery, a GC-MS analysis was performed on the samples used for RNA isolation and microarray profiling experiments described earlier. Over 300 metabolites were detected in shoot and root samples, including 135 polar compounds of which 100 were identified as known, and 165 nonpolar compounds of which 70 were identified as known. To determine which metabolites responded most to drought in shoot and root tissues, a PCA was performed. The mean values of all samples were applied to a PCA after log10transformation. The first three principal components derived from this data matrix encompassed 98.
2005; Nelson et al. 2007; Castiglioni et al. 2008; Karaba et al. 2007; Hu et al. 2006). With this work, we provide a thorough characterization of the transcriptomic variation induced by different stages of progressive drought stress, which has been included in the Medicago Gene Atlas server (http://mtgea. noble. org). Furthermore, we provide different sets of data showing positive and negative correlation of gene expression with drought stress that can be exploited by the scientific community and be used for translational genomics approaches in order to improve crop drought resistance.
The V. planifolia transcriptome was obtained from a 6-month-old vanilla pod from the island of La Reunion by 454 pyrosequencing. Approximately 40 UGTs, 15 OMTs, a CYP98A3 (C3H) and 4-HBS conreads were found in the transcriptome. To further assess the likelihood of involvement of each of these genes in vanillin biosynthesis, a targeted proteomic approach (proteomic mass finger printing) was carried out in parallel with the broad transcriptome analysis using the biosynthetically active inner part of the pod as experimental tissue. On the basis of overlay of the pyrosequencing and proteomic data sets, we selected and cloned 1UGT (VpUGT72U1), 11OMTs, a CYP98A3 orthologue (VpCYP98A70) and 4-HBS (Supplementary Table  1 ; Supplementary Data 1 and 2). Although in the literature, the vanillin biosynthetic pathway has been suggested to be embedded within a metabolic grid, our initial in vitro studies with these gene candidates identified a gene encoding an enzyme converting ferulic acid glucoside and ferulic acid directly into vanillin glucoside and vanillin, respectively.
In a number of experiments, vanillin formation was observed using feruloyl-CoA as a substrate. In such experiments, the incubation mixture was found always to contain ferulic acid present as an impurity in the commercially provided feruloyl-CoA. Since ATP and NAD þ were not required as cofactors in these reactions, we conclude that vanillin synthase is   not able to utilize feruloyl-CoA as substrate for vanillin formation by b-oxidation of the activated CoA ester  16. Accordingly, we conclude that VpVAN is catalysing vanillin and vanillin glucoside formation from ferulic acid and ferulic acid glucoside in a coupled non-oxidative hydratase/lyase reaction. A general amino-acid sequence identity search using GenBank showed that the VpVAN protein exhibits high sequence identity to cysteine proteinases.
The highest amino-acid sequence identity (77%) was found to the Elaeis guineensis cysteine proteinase belonging to the aleurain class of cysteine proteinases (MEROPSthe peptidase database). Interestingly, alignments unequivocally demonstrated that the VpVAN sequence contained the three key active site residues required for proteinase activity  25. Likewise the VpVAN amino-acid sequence contains the typical processing motif known from cysteine proteinases, indicating that the VpVAN protein when produced in the vanilla pod may be subject to a maturation cycle involving cleavage after the amino-acid residue at position 137 (DGV/LPVT). To test whether the activity of the VpVAN enzyme would be altered in the absence of the propeptide or if it changes the catalytic activity of the enzyme in vitro, we generated two truncated versions of VpVAN.
A sequence alignment of VpVAN with the HCHL sequence from P. fluorescens shows insignificant sequence similarity. Of the 55 conserved amino-acid residues scattered over the entire protein sequence in selected bacterial sequences belonging to the crotonase superfamily (see Achterholt et al. 39  , Fig. 5 ), only 11 were similarly positioned in VpVAN. The alignment with VpVAN identifies the position of the two consensus sequences involved in stabilizing the oxyanion hole in the crotonase superfamily. These show low sequence identity YGSEEE (residues 67-72) and QGI (residues 147-149) to the consensus sequences found in crotonases  38. A general sequence identity search using GenBank showed that the VpVAN protein sequence has a much higher sequence identity to cysteine proteinases. Cysteine proteinases are expressed as a pre-protein with an N-terminal ER-targeting signal peptide being part of a pro-peptide domain containing 130-160 residues  40.
qiagen. com) with on-column DNase I digestion. Quality of RNA was assessed using a bioanalyzer (Agilent). RNA (about 100 mg total) was provided to Eurofins MWG Operon (www. eurofinsdna. com) for 454 Roche sequencing. A normalized assembly of sequences was obtained. Obtained sequencing reads were de novo assembled using CLC Genomics Workbench 5. 0 with default settings. Raw sequencing reads were submitted to the Sequence Read Archive (SRA) database at National Center for Biotechnology Information (Bioproject accession no. SRP023166). Total RNA from Glechoma hederacea was isolated using the RNeasy plant kit (Qiagen) and provided to Macrogen (www. macrogen. com) for Illumina HiSeq sequencing. Raw sequencing reads were submitted to the Sequence Read Archive database at the National Center for Biotechnology Information (accession no.
KJ775791). Proteomic analysis. The inner part of the vanilla pod was ground to a fine powder in liquid nitrogen and extracted in 400 mM Tris/HCl (pH 8), 20 mM MgCl 2. Solubilized proteins were separated by SDS-PAGE on 10% Tris-glycine gels (Bio-Rad) and stained using Coomassie Brilliant Blue R-250 (Bio-Rad). Protein masses were estimated using a standard broad range Bio-Rad molecular mass marker. In-gel digestion of protein bands and MS were performed by the University of Victoria-Genome BC Proteomic center (method information found on www. proteincentre. com  48 ). The peptide mass data and tandem mass data obtained were used to search known protein sequences from the V. planifolia transcriptome data. Isolation and subcloning of genes. A complementary DNA (cDNA) library made from a 6-month-old V.
planifolia pod was kindly provided by Evolva A/S Denmark. The cDNA library was inserted in a pYES2 vector (Invitrogen) (http:// tools. invitrogen. com/content/sfs/manuals/pyes2_man. pdf). cDNA from Glechoma hederacea was made from material sourced in Basel, Switzerland. Total RNA was isolated using the RNeasy plant kit (Qiagen) and cDNA was made using the Mint2 cDNA synthesis kit (Evrogen) (www. evrogen. com). Candidate genes identified from the transcriptome data were amplified from the cDNA library by PCR with gene-specific primers (Supplementary Tables  1  and 3 ) to obtain full-length sequences. The PCR products were subsequently cloned in blunt-II-topo vector (Invitrogen) in E. coli. Plasmids were purified using the miniprep kit (Qiagen) and gene sequences were confirmed by sequencing.
Acknowledgements This work was supported by a grant from the  Danish Council for Strategic Research (DSF) , by a grant to the  VILLUM research center 'Plant Plasticity ' and by the  Center for Synthetic Biology : bioSYNergy supported by the  UCPH Excellence Programme for Interdisciplinary Research. Jørgen Hansen (Evolva A/S, Denmark)  is acknowledged for comments and corrections to the manuscript. We thank  BRC ,  VATEL ,  CIRAD, La Re  ´union for providing Vanilla planifolia materials. We thank  Hadrien Peyret  and  George Lomonossoff  for providing pEAQ-HT-DEST3 vectors for plant gateway cloning.
GC-MS spectra were obtained using the following conditions: the ratio split was 1:100, injection volume was 0. 4 µL and the carrier gas was helium. Injection temperature was 250 °C and the oven temperature range progressed from 40 to 250 °C at 2 °C•min -1 (for 60 min). The ionization mode used was electronic impact at 70 eV and the mass range between 35 and 400 was scanned. Essential oils were identified by comparison of their GC linear retention indices (RI), determined with reference to a homologous series of alkanes. Identification was confirmed by comparison of their spectral mass with authentic samples, with those stored in the MS database (home-made and commercial libraries: Wiley 6N, NIST 98) and with index retention literature data  [45]  using the Automatic Mass Spectral Deconvolution and Identification System (AMDIS) software.
The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to sup- port post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome. org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e. g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor.