dataesr/scientific-paragraphs-categorization huggingface dataset:
SEED MASS COMPARISONS The domestic forms were all landrace accessions, to exclude any effect of modern commercial breeding. For all crops, only wild and landrace seeds that were collected from the broad region in which the crop originated were included, to limit the inclusion of feral accessions of varieties developed by modern breeding. Both the seeds and the seed mass data available for beet are actually seed capsules, each containing one or two seeds in a tough, woody structure. We therefore dissected capsules after soaking in water for half an hour to soften them, and weighed 5-10 true seeds per accession. Seed masses typically follow a log-normal distribution  (Leishman et al. 1995) , and so data were log-transformed prior to analysis. Linear-mixed effects models were fitted for cereals, pulses, and vegetables independently, using the lme4 package in R.
annual grass (Poaceae) species exploited for their seeds. For each species, we list its geographical centre of domestication, Linnaean names of the domesticated landrace and its wild relative(s), literature sources to support the choice of wild relative(s) in each case, and use the taxonomy of Clayton et al. (2002). Sources of data and materials are listed with the following abbreviations: the USDA GRIN/NPGS database (GRIN); the Seed Information Database (SID) of The Royal Botanic Gardens, Kew; IPK Gatersleben (IPK); the International Rice Research Institute (IRRI); and the Australian Plant Genetic Resources Information System (AusPGRIS).
All are annual legume (Fabaceae) species exploited for their seeds (pulses). For each species, we list its geographical center of domestication, Linnaean names of the domesticated landrace and its wild relative(s), literature sources to support the choice of wild relative(s) in each case, and use the taxonomy of ILDIS (2005). All data and materials were sourced from the USDA GRIN/NPGS database (GRIN) or the Australian Plant Genetic Resources Information System (AusPGRIS) (Mung Bean only).
each species, we list the type of propagule used for cultivation (T, tuber or S, seed), its geographical center of domestication, Linnaean names of the domesticated landrace and its wild relative(s), and literature sources to support the choice of wild relative(s) in each case. Sources of data and materials are listed with the following abbreviations: the USDA GRIN/NPGS database (GRIN); IPK Gatersleben (IPK); EMBRAPA Genetic Resources and Biotechnology Centre (EMBRAPA); and the International Potato Centre (CIP).
For each species, we list the type of propagule used for cultivation (T, tuber or S, seed), its geographical center of domestication, Linnaean names of the domesticated landrace and its wild relative(s), and literature sources to support the choice of wild relative(s) in each case. Sources of data and materials are listed with the following abbreviations: the USDA GRIN/NPGS database (GRIN); IPK Gatersleben (IPK); EMBRAPA Genetic Resources and Biotechnology Centre (EMBRAPA); and the International Potato Centre (CIP).
All strains synthesized the ExlA protein, but strains lacking ExlB and either POTRA1 or POTRA2 were unable to secrete it into bacterial supernatants, as visualized by immunoblotting using anti-ExlA antibodies (Fig. 1B ). Consequently, the strains lacking ExlB or expressing ExlB without both POTRA domains were noncytotoxic (Fig. 1B ). Therefore, we concluded that ExlB is indeed the cognate partner of ExlA permitting its secretion, probably through the interaction between the POTRA domains and the N-terminal TPS signal of ExlA, as previously shown for the FHA and FhaC of B. pertussis  (21) (22) (23). The C-terminal part of ExlA, but not the five RGD motifs, confers on the protein its cytolytic activity. ExlA is a 172-kDa protein belonging to the family of polymorphic toxins  (24). In addition to the conserved secretion motifs based on an analysis in the Pfam database (http://pfam.
aeruginosa expressing ExlA. To that aim, we observed epithelial A549 cells infected with IHMA or its genetic variants by time-lapse microscopy. To follow the plasma membrane permeability, the infection was performed in the presence of YoPro-1, a membraneimpermeant dye (629 Da) that fluoresces upon interaction with RNA in the cytoplasm and DNA in the nucleus and can be used as a marker of small pores occurring during early apoptosis (Invitrogen). In A549 cells infected with ExlA-expressing strains, we observed and measured an increase of YoPro-1 fluorescence at early time points in the cytoplasm and later in the nucleus (as illustrated in Fig. 4A ). The data show an initial phase of slow fluorescence increase from 30 to 60 min corresponding to the complete entry of the dye in the cytoplasm.
Before infection, the RPMI medium was replaced with EBM-2 and the cells were labeled with vital Hoechst stain (1 g/ml) and YoPro-1 (1 M) followed by infection with the bacteria at an MOI of 10. Cell acquisitions were made using the ArrayScan high-content system (Thermo Fisher) every 5 min. Analyses were performed by measuring the fluorescence intensity of each cell using the HCS studio analysis software. Slopes were calculated between the 5 last time points before a sharp increase of fluorescence. The box plot was made using SigmaPlot software (Systat Software Inc. , San Jose, CA), and statistical analysis was done by the Kruskal-Wallis test. For confocal spinning-disk microscopy, the A549-EGFP cells were grown in RPMI medium supplemented with 10% fetal calf serum (all from Lonza). Cells were seeded at 25,000 cells per well on Lab-Tek II 8-chambered (Dutscher Scientific) coverslips and used 24 h later.
Cell membranes were labeled after incubation with WGA-Alexa 647 (Life Technologies) for 10 min at 37°C and then infected with bacteria at an MOI of 10 in EBM-2. Cell infections were observed by confocal spinning-disk microscopy for 4 h, with images recorded every 20 min. Successive planes in 3D stacks were taken every 0. 5 m. The 3D reconstruction was performed using the 3D viewer plug-in of ImageJ software. Analysis of ExlA secretion. Secretion of ExlA was monitored either in liquid LB cultures or under infection conditions. A 30-ml bacterial culture, in LB at an optical density at 600 nm (OD 600 ) of 1, was centrifuged at 6,000 rpm for 15 min. The supernatants (9 ml) were filtered, followed by addition of 90 l of 2% sodium deoxycholate (DOC). After a 30-min incubation at 4°C, 900 l of 100% trichloroacetic acid (TCA) was added and the proteins were allowed to precipitate overnight at 4°C followed by centrifugation at 15,000 ϫ g for 15 min at 4°C.
Analysis was done using MetaXpress software. Twitching motility assay. A determination of twitching motility by P. aeruginosa was carried out by inoculating bacteria at the interface between the plastic petri dish and LB agar (10 g/liter tryptone, 5 g/liter yeast extract, 10 g/liter NaCl, 1% agar). After 48 h of incubation at 37°C, agar was removed and the zone of twitching was revealed following Coomassie blue staining. Adhesion assay. A549 cells (5 ϫ 10 5 ) were cultured in 1ϫ RPMI with 10% FBS. Before the adhesion assay, A549 cells were treated with trypsin (0. 05% EDTA) for 2 min at 37°C, suspended in 1ϫ RPMI with 10% FBS, centrifuged at 2,000 rpm for 5 min, and suspended in EBM-2. Bacterial strains (5 ϫ 10 6 bacteria) were incubated with cells (MOI of 10) at 37°C with agitation. After 30 min, A549 cells and bacteria were centrifuged at 1,200 rpm for 5 min and pellets were resuspended in EBM-2.
ACKNOWLEDGMENTS We thank  Stewart Rudnicki  from screening facilities at  ICCB-Longwood ,  Harvard Medical School , Boston, MA;  Emmanuelle Soleilhac  from the  Screening Center for Bioactive Molecules (CMBA) ,  BIG ,  CEA-Grenoble ; and  Laëtitia Kurzawa , Life microscopy facility ( BIG, Grenoble ), for their help in training, setting up experiments, and data analysis. P. B. thanks  Xindan Wang  for help in using the colony-transferring robot (Hudson) ( Rudner Lab ,  Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA ). Pseudomonas aeruginosa strain IHMA87 was kindly provided by  International Health Management Association (IHMA; USA) , and Serratia strains were obtained from  J. Ewbank  ( CIML, Marseille, France ). We thank  Thomas Dougherty  for critical reading of the manuscript.
This work was supported by grants from  Laboratory of Excellence GRAL ,  ANR-10-LABX-49-01 , and  Agence national de Recherche   ANR-15-CE11-0018-01. P. B. received the Ph. D. fellowship from the  French Ministry of Education and Research , and E. R. received the  Ph. D. fellowship from Laboratory of Excellence GRAL. P. B. , M. R. , S. E. , E. R. , G. G. , S. B. , and E. F. performed experiments. P. H. , G. G. , E. F. , and S. L. contributed reagents. P. B. , S. E. , P. H. , S. L. , E. F. , and I. A. analyzed the data. P. B. and I. A. conceived the study and wrote the manuscript. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
The hydraulic piston nail penetrator was connected to a 5 bar air supply. All tests were carried out using the smart nail described above. The surface temperature of the 18650 cells was recorded using a thermal camera (FLIR SC5000MB, FLIR Systems France, Croissy Beaubourg, France). The thermal camera was operated in its high-temperature setting, which had a calibrated temperature range of 250 • C -1500 • C. The thermal camera had an infrared detection range of 2. 5 μm to 5. 1 μm on an InSb detector, and was shielded against high-energy X-rays by sheets of lead. The thermal camera was positioned ca. 30 cm from the penetration location, on the outer side of the sapphire window. The sapphire window had a transmittance of ca. 86% in the infrared range of 2. 5 μm to 5. 1 μm (data presented as Supplementary Information).
The 18650 cells were painted with a heat-resistant black paint with a calibrated emissivity of 0. 96. The nail penetration system and thermal camera were operated from the user-control room, outside the beam-hutch. X-ray imaging. -High-speed X-ray imaging of 18650 cells undergoing nail penetration was carried out at beamline ID19 at the ESRF. A polychromatic beam was used with a LuAG:Ce (Lu 3 Al 5 O 12 :Ce) scintillator and a high-speed PCO. Dimax camera (PCO AG, Germany). Two different frame rates were used: 2000 fps with an exposure time of 457 μs and a field of view (FOV) of 2016 × 1232 pixels with a pixel resolution of 10 μm, and 5310 fps with an exposure time of 44 μs, and FOV of 1344 × 668 pixels with a pixel resolution of 20 μm. Flat-field correction and time stamps were applied to the radiographs and the resulting images were compiled into movies using MATLAB.
Analysis of Bi-Stable Motion by Finite Element Method (FEM), MATLAB, and SIMULINK The frequency response of bi-stable motion was analyzed by the combination of structural and numerical analysis software. The structural analysis of our harvester was carried out by ANSYS 16. 0, as shown in Figure  2  Each beam is 15 mm-long, 30 μm-wide and 525 μm-deep. The central mass weights 0. 12 g. The structure material is silicon with Young's modulus of 180 GPa and density of 2. 33 g/cm 3. A zoom on Figure  2  shows that the whole non-linear spring is composed of a parallel pair of two beams separated by a 30 μm space. The resulting frequency response is shown in Figure  3. The bandwidth becomes wider depending on the applied acceleration. The natural frequency is 93 Hz. In the figure, the up-sweep frequency responses are shown in solid lines.
Study Design ONCEMRK (MK-0518 Protocol 292; ClinicalTrials. gov NCT02131233) was a double-blind, randomized, parallel group, noninferiority study comparing raltegravir 1200 mg QD with raltegravir 400 mg BID, each given with a fixed combination of emtricitabine 200 mg and tenofovir disoproxil fumarate 300 mg (FTC/TDF). The study was conducted according to Good Clinical Practice requirements and applicable statutes and regulations regarding the protection of human participants in biomedical research. An Independent Ethics Committee for each study site reviewed and approved the protocol, and the participants provided written informed consent before any study procedures were performed. Adults ($18 years of age) with screening HIV-1 RNA $1000 copies per milliliter and no previous antiretroviral therapy for treatment of HIV-1 infection were eligible for the study.
Exclusion criteria included documented or known resistance to any of the study regimen components and acute hepatitis or active infections other than chronic hepatitis B or C infection. Participants were randomly assigned (2:1) to raltegravir 1200 mg QD or 400 mg BID, each in combination with open-label FTC/TDF (TRUVADA; Gilead Sciences, Inc. , Carrigtohill, County Cork, Ireland) for up to 96 weeks. Randomization was stratified by screening HIV-1 RNA (#100,000 or. 100,000 copies per milliliter) and hepatitis B/C coinfection (yes or no). To conceal the treatment group assignment, participants also received placebo tablets matching the alternate treatment. Participants, study site investigators and staff, and sponsor personnel responsible for monitoring the study remained unaware of the treatment group assignments until the week 96 database lock.
Statistical Analysis The primary efficacy end point for this trial was assessed at week 48 and has been previously reported. 10 This report presents additional data to evaluate the secondary hypothesis that raltegravir 1200 mg QD is noninferior to raltegravir 400 mg BID, each in combination with TDF/FTC, as assessed by the proportion of participants achieving HIV-1 RNA ,40 copies per milliliter at week 96. A margin of percentage points was used to assess noninferiority. The week 96 hypothesis was tested sequentially after the week hypothesis was successfully met; therefore, the overall type I error was controlled at one-sided 2. 5% alpha level. The efficacy analyses used the Full Analysis Set population, defined as all randomized participants who received at least 1 dose of study treatment, with participants included in the treatment group to which they were randomized.
SAS version 9. 3 or 9. 4 was used for all analyses. For the analysis of the proportion of participants with HIV-1 RNA ,40 copies per milliliter, all missing data were treated as failures regardless of the reason, including early discontinuation of study therapy (Food and Drug Administration snapshot approach). The difference in proportions between treatment groups and the associated 95% confidence interval (CI) were calculated by the stratum-adjusted Mantel-Haenszel method. A supportive analysis of the proportion of participants with HIV-1 RNA ,50 copies per milliliter was also performed using the methods described above. For the analysis of change from baseline in CD4 + T-cell counts, missing data were handled with the Observed Failure (OF) approach. Baseline values were carried forward for participants who discontinued the assigned therapy because of lack of efficacy and for those who discontinued for non-treatment-related reasons and had HIV-1 RNA $40 copies per milliliter; participants with missing data for other reasons were excluded.
ACKNOWLEDGMENTS The authors thank the study participants and their families and caregivers for participating in the ONCEMRK study. The contributions of the investigators and their staff are likewise gratefully recognized, along with the following employees of  Merck & Co. , Inc. , Kenilworth, NJ:  Kim M. Strohmaier  for medical writing,  Carol Zecca  for editorial assistance, and  Danielle Mancaruso  for graphics support.
coli strains  [14]. Phylogrouping was performed in silico using the quadruplex method described by Clermont et al. [14]  and the primersearch program from the EMBOSS open software suite  [15]. E. coli BG1 belongs to the phylogroup B1, which is commonly distributed among both bovine commensal and human pathogenic E. coli strains  [16, 17]. A whole genome phylogenetic analysis based on single nucleotide polymorphism (SNP) differences in E. coli BG1, bovine and human commensal E. coli strains, bovine pathogenic E. coli strains and bovine O157:H7 STEC strains (Additional file 1: Table  S1 ) was conducted using CSI Phylogeny (version 1. 4)  [18]. Published E. coli genomes representing different E. coli pathotypes were selected for genomic comparison (Additional file 1: Table  S1 ). In addition, two reference E.
The Whole Genome Shotgun project was deposited at DDBJ/ENA/GenBank under the accession MOAH00000000 (Oct 31, 2016). A summary of the sequencing project information is provided in Table  2. Growth conditions and genomic DNA preparation E. coli BG1 was inoculated in Luria-Bertani broth from a single colony and incubated at 37 °C with shaking (200 rpm) to early stationary phase. The bacterial suspension was then centrifuged (10,000 g for 15 min) and the total DNA was extracted from the bacterial pellet using the DNeasy Blood and Tissue Kit following the manufacturer' s recommendations (Qiagen). DNA was quantified using a Nanodrop spectrophotometer and DNA integrity was electrophoretically verified by ethidium bromide staining.
Genome annotation The assembled contigs were annotated with Prokka (version 1. 10)  [22]  using standard parameters. Predicted genes were also assigned to functional categories of Clusters of Orthologous Groups (COGs) of proteins Fig. 2  Phylogenetic tree highlighting the position of E. coli BG1 relative to other E. coli strains. The whole genome SNP based phylogeny was established with CSI phylogeny 1. 4  [28]  using the genome of K71 as a reference and standard input parameters. The tree was midpoint rooted and plotted using Seaview (version 4. 6. 1) [56]. Each strain is identified as H (Human), B (Bovine), A (Avian), F (Food) or K12 (Laboratory strain), and its clinical or non-pathogenic (NP) characteristic is specified. using blastp against the NCBI COG 2014 database  [23]. Additional gene features were predicted using TMHMM Server 2.
Extended insights Genome repertoire comparison It is admitted that bacterial genome sequences show significant diversity due to horizontal gene transfers, gene loss and other genomic rearrangements  [1]. In this report, characteristics of whole genome datasets of a selection of E. coli strains were compared with those of E. coli BG1 (Table  5 ). Our main objective was to compare the genome of BG1 with that of bovine (K71 and W26) and human (SE15 and Nissle) commensal E. coli strains, but we also included a bovine pathogenic strain (VL2732) and a human EHEC pathogen (Sakai), as the bovine intestine is the main reservoir of EHEC  [10]. A human uropathogenic strain (NCTC9001 T ), which is also the E. coli type strain, was also included as reference. These strains were assigned to different phylogroups (Additional file 1: Table  S1 ; Fig.
Virulence factors The genes encoding virulence factors in the E. coli BG1 genome were analyzed using blastn against the Virulence Factors Database genomic dataset  [34]. A total of 164 genes encoding virulence factors were identified in BG1 (Additional file 2: Table  S2 ), while 181 and 202 genes encoding virulence factors were found in the reference strains NCTC86 and NCTC9001 T , respectively. In-depth analysis of the BG1 genome showed that most of these genes are involved in bacterial adherence to the host epithelium, iron acquisition systems (siderophores) and flagella synthesis. As expected, genes coding for toxins produced by pathogenic E. coli strains responsible for diarrhea or intestinal damage in mammals (Shiga-toxin, heat stable [ST] toxin, heat-labile [LT] toxin, heat-stable enterotoxin 1 [EAST1], cytotoxic necrotizing factor 1 [CNF1]) are absent in the BG1 genome.
Acknowledgements The authors thank  Frédérique Chaucheyras-Durand  for critical reading of the manuscript,  Alexandra Durand  and  Marine Bertoni  for excellent technical assistance,  Brigitte Gaillard-Martinie  for the transmission electron microscopy and  Olivier Bouchez  for genome sequencing. The genome sequencing was performed at the  GeT core facility, Toulouse, France  (http://get. genotoul. fr),and was supported by  France Génomique National  infrastructure, funded as part of the " Investissement d'avenir" program  managed by the  Agence Nationale pour la Recherche  (contract  ANR-10-INBS-09 ). We are also grateful to the  Genotoul bioinformatics platform Toulouse Midi-Pyrenées (Genotoul Bioinfo)  for providing computing and storage resources.
gravel bars either partially covered by vegetation in dense patches or totally covered by scattered vegetation; and floodplain, or all other landforms limited to the 10-year recurrence interval (CHD, 2010). We used the three cover types to perform two data analyses. First, the total area of each cover type was calculated in each segment to compare the net surface change between 2011 and 2014. Second, to elucidate the transitions between cover types, the amount of area that remained in the same cover type or changed from one type to another between 2011 and 2014 was classified into four categories of transitions: 1) polygons that remained as active channel type from 2011 to 2014 were considered permanent active channel; 2) transitions implying a change towards earlier stages in the morphological succession were considered rejuvenation, i.
At each transect, vegetation was recorded using the line-point intercept method  (Bonham 1989 ). All species intercepted on a vertical line from the ground to the tree canopy were identified and noted every 10 cm along each transect. This information was used to estimate the cover of each species at each site. When a species was present in different forms (heights) at the same sampling point, it was counted only once, such that the maximal cover value for a species at a given site was 100%. The number of pinpoints in a site ranged between 500 and 1500. Finally, data for substrate characterization was collected by randomly selecting a piece of gravel every 1 m along each transect to record the diameter of the intermediate axis ("b-axis" sensu  Krumbein 1941)  to the nearest millimeter. This information served to report the superficial grain size distribution  (Wolman, 1954).
, 2017b). Successful experiences like those reported here should not leave room for complacency but rather help design integrative conservation strategies for riparian zones that combine even more ambitious ecological-technical actions with socio-economic, educational, political and legal ones  (Gonzalez et al. , 2017b). Third, the data used in this study was collected only once (i. e. , one set of aerial photographs post-restoration, one field survey for vegetation) and therefore our study provides just a snapshot of a continuous process of ecosystem recovery. This consideration is especially important for rivers, where a great unpredictability of successional trajectories may be expected  (Hughes et al. , 2005). We recommend the implementation of monitoring programs durable enough (e. g.
Acknowledgments VMF was supported by a pre-doctoral scholarship from the  Ministerio de Educacion, Cultura y Deporte, Spain ,  FPU 2013. EG's participation in this project and field work were supported by a  Marie Curie International Outgoing Fellowship  within the  7th European Community Framework Programme  ( ESFFORES  project grant number  299044 ). We thank  Ignacio Santillan , responsible of the ecological restoration project of the Orbigo River at the  Confederacion Hidrografica del Duero , for his technical support. Prof. Eric Tabacchi  is gratefully acknowledged for his help to plant species identification. Comments by  Prof. Deborah Kennard  greatly contributed to improve the manuscript. We are grateful to two anonymous reviewers for their helpful comments on an earlier version of this manuscript.