dataesr/scientific-paragraphs-categorization huggingface dataset:
Luminometry was measured with a Spark reader (TECAN). Immunohistochemistry. Frozen sections (10 µm) were prepared from surgical skin biopsies. Slides were air-dried at room temperature overnight before acetone fixation for 10 min at room temperature. Sections were saturated with PBS containing 10% baboon serum, 2% normal goat and donkey serum, and 4% BSA. Sections were incubated overnight with primary Abs at 4 °C, followed by fluorescent secondary Abs as previously described  45, 69. T cell infiltration analysis was performed using rabbit anti-human CD3 Ab (Dako), and macrophage infiltration using a mouse anti-human CD68 Ab (clone KP1; Dako). Slides were analyzed with the AxioVision imaging software (Carl Zeiss, Le Pecq, France). Statistical analysis. Continuous variables were expressed as the mean ± SEM, unless otherwise indicated, and compared with the Mann-Whitney nonparametric two-sided test.
Acknowledgements This work was supported by the  French Public Bank of Investment (Effimab  grant  n°I 1302011  W), the  Fondation pour la Recherche Médicale  (grant number  LBS20130627235 ) and the  Région of Pays de la Loire. This work was realized in the context of the  IHU-Cesti  project, which received French government financial support managed by the  Agence Nationale de la Recherche  via the " Investment Into The Future" program   ANR-10-IBHU-005. The  IHU-Cesti  project is also supported by  Nantes Metropole  and the  Pays de la Loire Region. This work was also supported by the  FP7   VISICORT  project that has received funding from the  European Union 's  Seventh Framework Programme  for research, technological development and demonstration under grant agreement  602470. This work was realized in the context of the  LabEX IGO program  supported by the  National Research Agency  via the investment of the future program  ANR-11-LABX-0016-01.
The focus is on the full lifetime period of the medium resolution imaging spectrometer (MERIS) on board the ENVISAT satellite of the European Space Agency (ESA) from 2002 to 2012 (10 years). In particular, the aim is to quantify their spatial extension and intensity on the basis of water-leaving reflectance of MERIS. The paper is structured as follows. In the data and methods section, the study area, the data sets of remote sensing observations and in-situ measurements, the different methodological aspects and an error analysis on cloud effects are presented. In the results section, the remote sensed identified sulphur plumes are validated with in-situ measurements of H 2 S and S 0 found in the literature. The spectral properties of coastal sulphur plumes are derived by inter-comparison with reflectance products of satellite sensors with different spectral and spatial resolutions.
Satellite data Water-leaving reflectance. The reduced resolution (RR) Level-2 product of water-leaving reflectance (ρw) from the ocean colour sensor MERIS of the ESA satellite ENVISAT are used to study the spectral characteristics of sulphur plumes, in order to detect the coastal sulphur patches and their temporal variability. The data are available in the time period from April 2002 to April 2012 as daily scenes with a spatial resolution of 1 km × 1 km, through the MERIS Catalogue and Inventory (MERCI) system of the ESA. The data of the current processed 3 rd version are used. The water-leaving reflectances are continuously validated by the MERIS quality working group. Only their validation results for case 2 waters are relevant as the water masses of the considered study area belong to coastal optical complex waters  [36].
For case 2 waters, the official ESA data reprocessing validation report declares relative per cent errors (RPD) of < 12. 7% and root mean square errors (RMSE) of < 6. 11x10 -3 in the wavelength range between 412. 5 nm and 680. 9 nm  [37]. The RPD and RMSE are two statistical metrics to measure the uncertainties of water-leaving reflectance in the different MERIS channels (see  [38]  for definition). The only existing paper related to the Namibian Benguela upwelling area points to RPD smaller than 20. 0%  [36]. The water-leaving reflectance of MODIS (Moderate Resolution Imaging Spectroradiometer) of the Aqua and Terra platforms, HICO (Hyperspectral Imager for the Coastal Ocean) on the International Space Station and MSI (Multispectral Instrument) of Sentinel-2A (ESA Copernicus Programme) are also used for the investigation of the spectral characteristics of coastal sulphur plumes.
The MODIS and HICO data are available from the Ocean Biology Processing Group (https://oceancolor. gsfc. nasa. gov/), and the Sentinel-2A data from the Sentinels Scientific Data Hub (https://scihub. copernicus. eu/). Different spatial resolutions are available depending of the sensor (MODIS: 1 km, 500 m and 250 m, HICO: 90 m, MSI: 10 m, 20 m and 60 m). The channels in the visible spectral range were mostly used (MODIS-10 bands: 412. 5 nm to 678. 0 nm, HICO-56 bands: 404. 1 nm to 719. 1 nm every 5. 7 nm, MSI-9 bands: 443. 0 nm to 865. 0 nm). The MODIS Level-2 product of remote sensing reflectance (Rrs) was transformed to the water-leaving reflectance with the standard equation ρw = π Ã Rrs. For the work presented in this paper, the Level-1 products of HICO and MSI were processed to the Level-2 products of water-leaving reflectance with the software packages of SeaDAS (https:// seadas.
Quasi-true colour images of MERIS, MODIS, HICO and MSI derived from reflectance channels in the red, green and blue (RGB) were produced. These images are used for validation and comparison of remotely sensed identified sulphur plumes with in-situ measurements of H 2 S and S 0 in the studied area. Cloud fraction. The daily cloud fraction of MODIS Terra is available with a spatial resolution of 1˚, through the Goddard Earth Sciences Data and Information Services Center (GES-DISC). In the coastal region of the study area, the seasonal and annual area-averaged cloud fractions were calculated with the Interactive Online Visualization and Analysis Infrastructure (GIOVANNI, http://daac. gsfc. nasa. gov). We use these cloud fractions to investigate the impact of clouds on the sulphur plume time series.
For the calculation of our proxy for the upwelling intensity, the 4 μm SST product of MODIS Aqua measured at night time is chosen to minimize the effects of solar radiation and water vapour. The monthly SST data with a spatial resolution of 4 km are available through the systems of GES-DISC and GIOVANNI. The nearest coastal area limited by the two main upwelling cells of Walvis Bay and Lu ¨deritz  [45]  is taken into account for the calculation of the upwelling intensity because the sulphur plumes are mainly observed in these regions  [46]. To do so, the coastal SST values are averaged over the box from 23˚S-28˚S and 14. 3˚E-15. 6˚E. Moreover, SST data of TMI (TRMM Microwave Imager) with a spatial resolution of 25 km are applied to check the MODIS SST  [47]. The monthly TMI data are available from the Remote Sensing Systems (http://www.
To do so, the wind values are averaged over the box from 23˚S-28˚S and 13. 3˚E-15. 6˚E. The RMSE in wind speeds of TMI, QuikScat, ASCAT, and CCMP are 0. 8-1. 6 m s -1 [57, 58], 1. 0-1. 7 m s -1 [59-61], 0. 1 m s -1  [62]  and 0. 8 m s -1  [56] , respectively. Sea level anomalies. The sea level anomalies (SLA) from the gridded AVISO + product (Archiving, Validation, and Interpretation of Satellite Oceanographic project) are used in this paper. We take the merged product made with the altimetry sensors (T/P, ERS, ENVISAT, Jason) available for the 2002-2012 time period. The SSALTO/DUACS product (Ssalto multimission ground segment/Data Unification and Altimeter Combination System) distributed by CMEMS (European Copernicus Marine Environment Monitoring Service) is used with a daily frequency on a 1/4˚Cartesian grid (http://www.
In-situ measurements In-situ measurements of H 2 S and S 0 in the water column are used for validation (Fig  1 ). These measurements are compared with our produced sulphur plume products derived from remotely sensed data. Only few in-situ data are available in the Namibian coastal area over the 2002-2012 period. In the year 2002, Weeks et al. [16]  measured eight times the concentrations of H 2 S (see the locations of stations M1 to M3 in Fig 1 ) in the surface water layer during satellite overflights. However, the concentrations of S 0 (first 10 m depth) were measured only one time during sulphur plumes. Lavik et al. [10]  measured the bottom water concentration of H 2 S over a large area of about 7000 km 2 in January 2004 (colored isolines in Fig 1 ), a year with high activity of coastal sulphur plumes  [46].
The basic method introduced by Ohde et al. [46]  is improved and their implementation in the software package of the interactive data language (IDL) is updated in this paper. We explain in the following our improved methodology: 1. The full time period of the MERIS sensor from April 2002 to April 2012 are processed. 2. The study area is extended to the coastal area between 18˚S and 28˚S. 3. The water-leaving reflectance of MERIS of the current 3 rd version is used.
Daily satellite swaths are combined to single MERIS scenes if different swaths overlaying the study area for the same day. The scenes are gridded to the same Mercator projection by the ESA-Sentinel Application Platform (SNAP). 5. The four conditions for the detection of sulphur plumes defined in Ohde et al. [46]  are adapted to the 3 rd reprocessing by the definition of new threshold values using the full MERIS data set. The first condition ρw (412. 5 nm) < ρw (442. 4 nm) are not changed. The second (ratio ρw (664. 6 nm) to ρw (680. 9 nm)) and third (peak value of ρw (559. 6 nm)) conditions are adapted only slightly. Now the threshold values of 1. 0054 (old: 1. 0146) and 0. 0400 (old: 0. 0479) are applied. The fourth condition is modified using the full MERIS data set of 2002 to 2012. Now the slope between ρw (559.
Acknowledgments This study has received funding from the  European Union 's  Horizon 2020 research and innovation program  under the  Marie Skłodowska-Curie  grant agreement No  706426. The authors thank the host institute  OMP/LEGOS (Observatoire Midi-Pyrenees/Laboratoire d'Etudes en Geophysique et Oceanographie Spatiales) in France  for their support. This investigation was mainly based on satellite data of different sources. The MERIS and MSI data were kindly provided by  ESA. We acknowledge the use of MODIS data from  LANCE FIRMS  operated by the  NASA/GSFC/Earth Science Data and Information System (ESDIS)  with funding provided by  NASA/HQ. Data products of the Ocean Biology Processing Group (OBPG) were used (HICO, VIIRS, MODIS). TMI, QuikScat, ASCAT and CCMP data were produced by  Remote Sensing Systems (RSS)  and sponsored by  NASA.
Fig. 6c  shows that the chemical composition of this area is similar to that of the bulk material without inclusion. Therefore, the interior crack initiation of the present TC11 might be associated with microstructural inhomogeneities. This point will be checked in our future work. Furthermore, the surface roughness of the fisheye, as shown in Fig. 6 , was analyzed by a surface profilometer (VeecoWyko NT1100) to derive quantitative geometric morphology information of the FGA and the flat surface in the fisheye region. Fig. 7  shows the 2D graph and the corresponding 3D scan from the surface profilometer of a 1. 20 mm×0. 93 mm area. The mean surface roughness Ra of the FGA and the other region in the fisheye is approximately 32 μm and 3. 4 μm, which was measured and calculated automatically by Vecco vision software.
Acknowledgements The authors thank  King Abdullah University of Science and Technology ,  Badische Anilin  and  Soda Fabrik ,  Engineering and Physical Sciences Research Council  Project  EP/G037515/1 ,  EP/M005143/1 ,  EP/N509486/1 ,  EC FP7  Project  SC2  ( 610115 ), and  EC H2020  Project  SOLEDLIGHT (643791 ) for the financial support.
Moths' sampling and rearing In the present study, we sequenced RNA from adult moths sampled from a previous experiment  (Orsucci et al. , 2016) , where phenotypic and behavioral traits of moths facing different plant environments were measured. The whole experimental framework is reminded in Box 1 ("experimental design" session). Briefly, around 20 males and females were released in three types of conditions: (i) 'choice' cages, with maize and mugwort plants, (ii) 'maize' cages (usual host for ECB) and (iii) 'mugwort' cages (usual host for ABB). After 72h, several life history traits and particularly the egg laying were quantified. After measurements, all adults were recaptured and the females were used for the acquisition of expression data by RNA sequencing (see Fig. Box 1 ).
De novo transcriptome assembly and annotation After sequencing, all reads were subjected to quality control and trimming using Trimmomatic v0. 25 to remove Illumina sequencing adapters and low quality reads  (Bolger et al. , 2014). Ribosomal and bacterial contaminants were removed using sortmeRNA v2. 0, and Bowtie2  (Langmead & Salzberg 2012; version 2. 2. 4 ) mapping against a bacteria subset dataset extracted from NCBI database (October 2014). To obtain two comprehensive transcriptomes from ECB and ABB libraries, we first assembled the high quality reads of the 12 ECB libraries on one side and of the 12 ABB libraries on another side using the trinity program suite  (Haas et al. , 2014)  using default parameters and normalization. Then, for each of the resulting ECB and ABB assemblies, we included 454 data previously obtained by  Gschloessl et al.
(2013)  from 4 ECB and 4 ABB adults, respectively. To achieve this goal, we used the EMBOSS  (Rice et al 2000)  splitter program (version 6. 6. 0) to create short overlapping subsequences (length 300 bp, overlap 200 bp) for each of the 454 transcripts and the HiSeq transcript sets, respectively. All 454 and HiSeq subsequences were then assembled with Newbler (454 Life Sciences Corporation, v 2. 9) with 40 bp minimum overlap length, 97% minimum overlap identity and the 'Het' (for heterozygote) options. Finally, we selected the longest transcript as representative sequence for each gene to circumvent the occurrence of putative alternative transcripts that might bias expression analyses. For functional and GO-terms annotations, a custom script was developed to compare ECB-ref and ABB-ref genes to NCBI nr (version may 2016) and UniprotKb  (Bateman et al.
Candidate sensory genes In parallel to the de novo transcripts' reconstruction, we compiled a set of 141 reference genes involved in sensory perception previously described in ECB, ABB and related species of the Ostrinia genus  (Leary et al. , 2012; Miura et al. , 2009; Miura et al. , 2010; Wanner et al. , 2010; Yang et al. , 2015)  composed of: odorant receptors (ORs), gustatory receptors (GRs), ionotropic receptors (IRs) sensory neuron membrane proteins and odorant degrading enzymes. As some of them may be orthologs between species, or similar between the studies, we removed the redundant sequences as identified by a reciprocal blast analyses. After this filtering step, the sensory dataset was reduced to 139 unique sequences (Table  S2 ). This gene set, hereafter called 'Senso-ref', was used as an independent gene reference from ABB-ref and ECB-ref to focus on sensory genes.
Raw reads mapping and normalization Raw reads were mapped onto ABB-ref, ECB-ref and Senso-ref using Bowtie2  (Langmead & Salzberg 2012; version 2. 2. 4 ), with default parameters and "sensitive" option. After the mapping, we produced the counts of mapped reads per gene with samtools program  (Li et al. , 2009). Transcripts-specific variations (dispersion and logarithmic fold-changes of reads counts among experimental conditions) were estimated with the Bioconductor edgeR (Empirical Analysis of Digital Gene Expression Data in R) package  (Robinson et al. 2010; version 3. 8. 6). A negative binomial distribution was chosen as model for counts variations, and transcripts with less than one count per million for at least half of libraries were removed. Reads counts were normalized among conditions (i.
Transcripts were considered differentially expressed (DE) in the whole experiment if they had a false discovery rate (FDR) adjusted p-value < 0. 01. Gene ontology (GO) enrichment was calculated in R using "top GO" package (v2. 26. 0) from the Bioconductor project (Alexa and Rahnenfuhrer, 2010). We used the GO annotation described previously as 'custom input'. We removed GO terms with fewer than 5 annotated genes (using the nodeSize parameter set to 5). We used the 'weight' algorithm and the Fisher exact test procedure. We report enriched GO categories with p-values < 0. 01 for the following DE gene lists: DE genes between ECB and ABB species, and DE genes between experimental environment (maize and mugwort, maize and choice, mugwort and choice).
ECB-and ABB-ref assemblies and annotation The main features of the raw read data and ECB and ABB assemblies (HiSeq only or HiSeq-454 combined) are detailed in Table  1. We observed that the combination of published 454 transcripts and de novo HiSeq transcripts has doubled the length of transcripts (Table  1 ) compared to the solely de novo HiSeq assembly. Taking the longest sequence as unique represent for each unigene resulted in 9,415 ECB genes and 9,992 ABB genes (Table  1 ). Homology searches in genomic and protein databases yielded significant hits for 61% of the ECB genes among which 80% had an associated GO term. More than 97% of the annotated genes were homologous to Lepidoptera genes, followed by homologs to other insect orders (Table  S3 ). To a much lower extent, hits with genes of plants, viruses and bacteria were also observed.
Acknowledgments We thank  Béatrice Ramora ,  Anne Zanetto  and  Christophe Reynaud  for technical assistance in plant cultivation in DIASCOPE (experimental research INRA station) site. We thank also  Denis Bourguet ,  Pascal Milesi  and  Carole Smadja  for their critical and helpful comments on the manuscript. This work received supports from  ANR Adapt-Ome  ( ANR-13-BSV7-0012-01 ) to RS and DB, from the  INRA department 'Santé des Plantes et Environnement ' and from the  University of Montpellier  for MO PhD studentship.
To remove contribution of partial volume artifacts around the staples to the vascular segmentation volume, the output binary staple volume was "dilated" by five voxels and removed/subtracted from the segmented vascular volume. Subsequently, vessel and staple binary volumes were skeletonized using 3D thinning algorithms that reduced these structures to single voxel thick lines (MatLab R2011b, MathWorks, Natick, MA, USA). This was performed to prevent possible over-estimation of perfusion when thicker or clumped vessels are prevalent and potentially dominate volumetric measurements. For delineation of a region of interest (ROI) for analysis, all three staple rows within the segmented staple volume were morphologically "closed" filling in spaces between rows to create a single solid object that "wraps" around all staples.
Background: There are randomized trials assessing a variety of antiviral drugs for hepatitis B virus (HBV), but the relative effectiveness of these drugs in the treatment of patients co-infected with human immunodeficiency virus (HIV) remains unclear. The objectives of the current study were to estimate and rank the relative effectiveness of antiviral drugs for treating HBV and HIV co-infected patients. Methods: Randomized trials, assessing the efficacy of antiviral drugs for HBV and HIV co-infected patients were searched in health-related databases. The methodological quality of the included trials was evaluated using the Cochrane risk of bias tool. Main outcome in this meta-analysis study was the success of treatment by antivirals as determined by virologic response. We performed pairwise and network meta-analysis of these trials and assessed the quality of evidence using the GRADE approach.
Search Relevant RCTs were searched in the health-related databases of Ovid MEDLINE, Ovid Embase, The Cochrane Library, and Google Scholar. The search strategies for the Ovid MEDLINE are given in Additional file 1. Our search was restricted to publications in the English language up to February 2018. To identify ongoing or completed trials, we also searched in ClinicalTrials. gov (http:// www. clinicaltrials. gov/), WHO International Clinical Trials Registry Platform (http://apps. who. int/trialsearch/Default. aspx) and EU Clinical Trials Register (https://www. clinicaltrialsregister. eu/). We did not search for the adverse effects of antiviral drug interventions separately and only used data contained in the publications identified for the present study.
Data extraction Two review authors independently screened the titles and abstracts of citations from the electronic database search and retrieved full-text of all potentially relevant articles. When studies had duplicate publications, we extracted the maximum amount of data from the available publications. The two review authors then independently checked the full-text articles for eligibility based on the inclusion criteria. The two reviewers extracted data from the included studies using a piloted data extraction sheet. Data collected were authors, country, publication year, participant's characteristics, details of intervention and controls regimen (dosage, route of administration, frequency and duration), outcomes, method of outcome measurements, follow-up time points of the outcome and adverse events.
Nel primo caso, la figura del coautore traduce la volontà di dare voce agli attori più 'umili' della storia. In effetti, bisogna notare che soltanto i testimoni provenienti dalle classi superiori testimoniano nell'intervallo fra il 1945 e il 1963 (figura 1). Figura 1 Le testimonianze secondo la presenza del coautore e la data della pubblicazione Quando si tratta di una testimonianza diretta, essa è il risultato della volontà propria del reduce, che pensa di disporre delle capacità linguistiche sufficienti. Questa consapevolezza va di pari passo con un senso di legittimità che emerge nel testimone. Tali testimoni dispongono in maniera generale di un capitale simbolico 20 (indicatore della loro posizione sociale) superiore a quello dei testimoni provenienti dalle classi popolari (figura 2). 21 Si tratta di individui che scrivono e al tempo stesso riflettono sulla propria esperienza concentrazionaria (in queste testimonianze è manifesta la combinazione fra le descrizioni dell'evento vissuto e la sua analisi) e che occupano o addirittura rivendicano il proprio posto nello spazio pubblico.
Introduction Over the last 2 decades, the concept of global observing systems and the importance of defining user requirements for the purpose of monitoring and forecasting elements of the Earth system have gained momentum. This also applies to atmospheric composition in general and aerosol in particular with the studies of  Barrie et al. (2004)  for atmospheric composition monitoring,  Reid et al. (2011)  for operational aerosol forecasting,  Benedetti et al. (2011)  for operational verification of aerosol properties, and  Colarco et al. (2014)  for the use of Earth Observing System data for aerosol operational systems. Indeed, at the time of writing this document, there are at least nine operational centers producing and distributing real-time global aerosol forecasting products, including ECMWF Copernicus Atmosphere Monitoring Service (CAMS), Finnish Meteorological Institute (FMI), Fleet Numerical Meteorology and Oceanography Center (FNMOC), Japan Meteorological Agency (JMA), NOAA National Centers for Environmental Prediction (NCEP), and UK Met Office.