dataesr/scientific-paragraphs-categorization huggingface dataset:
0 stores 3D emission densities as sparse matrices. Figure  7 (a) shows the field of view of an experimental camera. The grayscale image was taken from a shot with a disruption flash in which the JET wall is well visible. By fitting selected image points with corresponding points on the JET 3D wall geometry model using the Python package CALCAM  10  , the camera parameters such as the pupil position and LOS could be obtained. Figure  7 (a) illustrates the alignment of experimental images with the synthetic ones. One can see that there is misalignment in some image regions (mostly on the image borders where optical aberrations are the strongest), however the relevant image regions where Be emission occurs are well aligned. As no Be emission images were available from the density scan experiment, instead we use images measured parasitically in limiter discharges (reference shot JPN #91140) with the plasma shifted upward compared to JPN #80321.
The plume width is determined mostly by the ionization rate for Be 0 or Be + , which in turn is given by the product of the corresponding ionization rate coefficient (obtained from the ADAS code database  [29] ) and n e. While the rate coefficient shows only a slight dependence on n e and T e in the parameter range of interest, an underestimation of the electron density n e in the plasma background may well account for the too broad emission plume. A more thorough benchmarking would require comparison to BeI experimental images which were not available at the time of writing this manuscript. Finally in region III, an emission plume is visible in the experimental image below the IWGL in octant 5Z, which is missing from the synthetic image. This can be attributed to erosion of the Be parallel protection bars  [2] , which are currently missing in the ERO2.
The background ion flow velocity, which is directed towards the closest PFC along a field line in the SOL, was previously shown to play an important role in non-local Be transport  [19]. Therefore, the 3D ion flow field in the SOL was calculated here using the 'simple SOL' model (equation  (3. 9c ) in  [30] ). Outside the SOL it was assumed to be zero. To improve the ERO2. 0 simulations, dedicated modeling of JET limiter plasma backgrounds using the edge code SOLEDGE2D  [31]  is currently ongoing. The new plasma background are expected to provide more accurate values of n e and T e as well as information about ion temperature, flow velocity and electric fields. Benchmarking with further experimental diagnostics, such as Z eff measurements, wideview 2D camera images and LOS-integrated signals for various BeI and BeII emission lines, and IR cameras, should be performed in order to reduce model uncertainties and further increase confidence in predictive modeling for ITER.
Acknowledgments This work has been carried out within the framework of the  EUROfusion Consortium  and has received funding from the  Euratom  research and training programme  2014-2018  under grant agreement No  633053. The views and opinions expressed herein do not necessarily reflect those of the  European Commission. The authors gratefully acknowledge the computing time granted by the  JARA-HPC Vergabegremium  on the supercomputer JURECA at  Forschungszentrum Jülich.
Apparatus An EyeLink 1,000 eye tracker (SR Research Ltd. ) was used to measure eye position and pupil size. The eye tracker had a sampling rate of 1,000 Hz and used an automatic saccade-detection algorithm based on a velocity threshold of 30 • /s and an acceleration threshold of 8,000 • /s 2 , which corresponds to the configuration for the EyeLink 1,000 for cognitive research. Stimuli were presented on a ViewSonic P227 monitor with a refresh rate of 100 Hz and a screen size of 1,024 × 768 pixels. Participants were seated at a viewing distance of 80 cm. Stimulus presentation was controlled with Experiment Builder software (SR Research Ltd. , Ottawa, Ontario, Canada). Eye movements were recorded from the right eye. Pupillary size was measured as pupillary diameter. The pupillary size data is not calibrated, and the units of pupil measurement will vary with subject setup.
Data analysis approach Our analyses focus on the correlation between pupil size and the saliency of fixated locations (see Saliency analysis). Mathôt et al. (2015)  previously reported that this correlation is reliably negative. That this, they found that people are more likely to look at low-salient locations when their pupil is large. Here we investigate whether this correlation differs between experts and novices. In the current study, participants were invited to view dynamic scenes, thus the potential for pupil measurements is expected to be skewed by the angle of the eye, a factor also referred to as pupil foreshortening error (PFE), which is likely to produce a group-effect in pupil size data driven solely by group differences in gaze locations. Given that the patterns of eye movements in this study are expected to systematically differ across the two groups, we have opted for a correction for PFE in the pupil data in order to avoid spurious regularities  (Gagl, Hawelka & Hutzler, 2011; Hayes & Petrov, 2016).
Linear mixed effects analysis Linear Mixed Effects (LME) (e. g. ,  Baayen, Davidson & Bates, 2008; Bates, 2005)  modeling was conducted with the corrected pupillary diameter (cPD) as a dependent variable and Saliency, Expertise (novices vs. experts) and video Complexity as independent variables. The following multiplicative LME model formula was implemented: cPD ∼ Saliency × Expertise + (1|subjects) + (1|videos) (as random effects on the intercept) using the lmerTest package of the R software (The R Development Core  Team, 2009). The ''subjects'' and ''videos'' terms fit random variation between participants and videos in the experiment given the large size of repeated measures that can be extracted from the video stimuli and the conservative criteria we applied that resulted in the selection of few participants in terms of their expertise.
The fixations distribution analysis As mentioned above, eye fixations are used in previous studies as an additional index to compare between experts and novices with respect to their strategies. Hence, we compared in this analysis between the fixation distribution for experts and novices averaged on over all trials. Figure  3  represents two heatmaps for experts and novices with the spatial distribution of all data points relative to their eye fixations as defined by x and y coordinates on the screen with time being collapsed. According to Fig. 3 , experts seemed to be more focused on particular areas than novices and oppositely attributed importance to some spatial regions on the screen. Figure  4  shows two perspective plots of the probability density function (see  Castet & Crossland, 2012  for similar use) of the fixation points represented in Fig.
We used Bayesian clustering (STRUCTURE software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.
g. , Hardy Weinberg and linkage equilibria, and have previously proven useful for investigations of demography and genetic structure  (Kraus et al. 2013)  as well as for addressing evolutionary questions such as genetic introgression and speciation  (Kraus et al. 2012). As a genotyping platform, we used the Illumina GoldenGate Genotyping Assay on the Illumina BeadXpress, with accession numbers ss263068950-ss263069333 in dbSNP for the set of 384 SNPs. When possible, we put 5 μl of 75 ng/μl of DNA per genotyping reaction, and a minimum of 50 ng/μl. Samples at a lower concentration were checked for an excess of missing data and eventually excluded when required (see BResults^section for thresholds). Raw data were analyzed in GenomeStudio (Illumina Inc. ). We also tested for a bias in homozygosity between historical museum samples versus contemporary ones that could arise through allelic dropout.
In addition, K = 3 show that Czech farmed mallards (red) are clustered separately from other farmed birds (yellow), and for K = 4, all farmed mallards (Swedish: green; French: yellow; Czech: red) are separate clusters. Throughout higher levels of K, the assignment of mallards from farms to the farm clusters remains stable, while the resolution of wild mallard clusters is obscured Hemisphere and analyzed with the same SNP set by  Kraus et al. (2013). A total of 32 SNPs were excluded to make the two datasets comparable (Table  S2 ). This analysis was run in STRUCTURE with all samples pooled and the same settings as for the present analysis.
Acknowledgements We are grateful to The  Swedish Museum of Natural History in Stockholm, The Museum of Evolution in Uppsala, The Natural History Museum in Gothenburg, The Bird Museum in Jönköping, The Museum of Zoology in Lund, Tromsø University Museum, The Natural History Museum in Helsinki, Kuopio Natural History Museum, The natural history museums in Paris, Toulon, Avignon, Aix en Provence, Nîmes, Marseille, Istres, Gap, Digne, Saint Gilles, Montpellier, Salon de Provence, Port St-Louis du Rhône, Nantes, La Rochelle , to the  Department of Zoology of the National Museum in Prague, The Moravian Museum in Brno, The Čáslav museum, The Regional Beskyd Museum in Frýdek-Místek, The Museum of Ostrava, The Regional Museum in Teplice, The Regional Museum in Olomouc, The Ornithological Station of the Comenius Museum in Přerov, The Museum in Ústí nad Labem, The Museum of South-East Moravia in Zlín, The East Bohemian Museum in Pardubice, The Museum of the Labe Region in Poděbrady  and their respective curators, as well as to owners and curators of private collections: Tour du Valat and Restaurant Ble Flamant rose^for access to their collections.
We found that only the HST/STIS Echelle spectra provide the necessary wavelength accuracy (1 km•s -1  [25] ) needed for this project. In addition to G191-B2B (the object studied in  [14] ), we identified nine hot, bright white dwarfs and sub-dwarfs. We were also awarded 12 orbits with HST/STIS (scheduled for autumn 2017) to obtain new far-UV observations of three bright white dwarfs known to have photospheric Fe and Ni absorption lines. Table  1  provides an overview of the 13 objects that will be studied in the course of this project. Our sample includes objects with gravitational potentials spanning four orders of magnitude. We examine the spectral data of each object before fitting the absorption lines to identify the FeV and NiV transitions relevant for estimation of ∆α/α. All transitions were visually checked for obvious cases of blends, and where found, those transitions were discarded.
In addition, for the purposes of the preliminary results in this paper, we confine ourselves to using the FeV and NiV transitions listed in  Berengut et al. (2013)   [14]. However, we use the three new laboratory wavelengths (the Kramida, Tchang-Brillet, and Nave wavelength lists) available for these transitions as discussed above. We fit the absorption spectra in the normal way, using the Many Multiplet method and the software VPFIT 1 For each object, we initially construct a Voigt profile model (by visual inspection) with a single velocity component (absorption line), including all suitable transitions. We then apply VPFIT to optimise the Voigt profile parameters, including ∆α/α as a free parameter in the fit. Statistical uncertainties are determined from the diagonal terms of the covariance matrix at the best-fitting solution.
Acknowledgments: We thank  Gillian Nave  ( NIST ) and  Jacob Ward  ( NIST ) for providing preliminary FeV and NiV wavelengths prior to publication. This research used the  ALICE High Performance Computing Facility at the University of Leicester. This project is funded by a  Leverhulme Trust   Research Grant. WULTB wishes to acknowledge support from the  LABEX Plas @par managed by the  French ANR  ( ANR-11-IDEX-0004-02 ). J. D. Barrow  is supported by the  STFC  of the UK.
The molecular environment of Ni and Fe was probed by using extended X-ray absorption fine structure (EXAFS) spectroscopy. EXAFS spectra of the pyrite end products were least squares fitted to theoretical ab initio spectra calculated with the Feff8. 1 code. EXAFS spectra of the solids collected over the course of the experiments were analysed by linear combination least squares (LC-LS) fitting using a large model compounds spectra database  (Noël et al. , 2014 (Noël et al. , , 2015)). Detailed procedures are reported in Supplementary Information.
9 mol. % Ni ideal; Fig. 4b  and Table S-6 ) with respect to the aqueous Ni/Fe ratio (0. 013 mol. %) measured by ICP at the end of the lag phase. This enrichment that agrees with so-called "common salt effect" is consistent with the x value of 5. 4 mol. % Ni observed for the first pyrite nuclei that formed after 24-29 hours, as calculated by combining EXAFS (Fig. 2  and Table  S-3)  and aqueous chemistry data (Table S-6 ). The x value of the pyrite overgrowth is then expected to have rapidly decreased after 48 hours, as confirmed by EXAFS (Fig. 4b  and Table  S-6 ), and to have almost vanished after 100 hours of synthesis (Fig. 4b  and Table  S-6 ). The compositional zoning of our synthetic Ni-doped pyrite nanocrystals (Fig. 3 ) can hence be interpreted as successive overgrowth of ideal solid solutions with decreasing Ni substitution rate.
Acknowledgements This study was funded by an  ANRT-UPMC/CNRS/IRD/ IPGP-KNS  collaborative research programme. We are greatly indebted to  S. Capo  (KNS),  G. Marakovic  (KNS), and  C. Marchand  ( IRD ) for the field part of the programme published elsewhere. We acknowledge the help of  I. Esteve  ( CNRS ) for  SEM, L. Delbes (UPMC)  and  F. Gélébart  ( CNRS ) for anoxic XRD,  L. Cordier  ( Univ. Paris 7 ) for  ICP-AES, A-L. Auzende (Univ. Genoble-Alpes ) for TEM analyses. E. Fonda ,  V. Briois  at  SOLEIL ,  Olivier Mathon  at  ESRF  and  M. Munoz  (CNRS), are greatly acknowledged for their technical support during EXAFS measurement.
4% vs 5. 7%; OS: 23. 3 months vs 18. 9 months; hazard ratio [HR]: 0. 79 and P=0. 051). This led the US Food and Drug Administration (FDA) to approve Imlygic ® , the first FDA-approved oncolytic virus therapy, at the end of October 2015, for the treatment of melanoma lesions in the skin and lymph nodes and subsequently to the European Medicines Agency (EMA) approval. Pexa-Vec (pexastimogene devacirepvec, JX-594) is an oncolytic and immunotherapeutic vaccinia virus engineered to express GM-CSF. Pexa-Vec mechanisms of actions include tumor cell infection and lysis,  [19] [20] [21]  antitumor immune response induction  22, 23  and acute vascular disruption. 24 Pexa-Vec is derived from the commonly used Wyeth vaccine strain (Dryvax ® ; Wyeth Laboratories, Dallas, TX, USA). In a randomized phase 2 study (HEP007, NCT00554372) in advanced first-line hepatocellular carcinoma (HCC), a significant improvement in OS (HR 0.
39, P=0. 02) was observed with Pexa-Vec at 10 9 pfu (14. 1 m) vs 10 8 pfu (6. 7 m). 22 exa-Vec has now entered a randomized controlled phase 3 trial in advanced first-line HCC (NCT02562755), comparing the administration of Pexa-Vec and sorafenib to sorafenib alone, with OS as the primary end point. The oncolytic vaccinia viruses JX-GFP and TG6002 were used in the studies described here. JX-GFP is derived from JX-594 and modified by insertion of a gene cassette in the thymidine kinase (TK) locus expressing green fluorescent protein (GFP) and human granulocyte-macrophage colonystimulating factor (hGM-CSF). Inactivation of vaccinia TK attenuates JX-GFP in normal cells, which have lower levels of cellular TK. In contrast, in cancer cells, endogenous TK is typically overexpressed so that the virus can continue to replicate.
After 1 h, cells were washed, and secondary antibody (PE or FITC goat anti-mouse IgG [minimal x-reactivity] antibody, BioLegend ® , San Diego, CA, USA) was added and incubated for 1 h. Cells were gated on Annexin-positive, propidium iodide (PI)-negative cells for further analysis on surface calreticulin expression. In DC coculture experiments with tumor lysates, cells were harvested and stained with anti-CD80 APC, -CD83 PE and -CD86 PE antibodies (BD Biosciences Pharmingen). The expression of these receptors on DCs was analyzed on a FACSCalibur flow cytometry system (BD Biosciences). Fluorescence was measured with a minimum of 15,000 events per sample. Data analysis was performed using the Cell Quest Pro software (BD Biosciences). elisa Supernatants of cocultivated cells were collected before harvesting and stored at -80°C.
Type of cell death, apoptosis and necrosis To define the type of cell death which is induced by the vaccinia viruses, we performed an apoptosis assay with FACS staining of phosphatidylserine via Annexin V and DNA via PI. Early apoptotic cells express phosphatidylserine, while the DNA of necrotic cells could be stained with PI and a combined signal of both could be associated with late apoptosis. 5-FC and 5-FU treatments were added in the experiment to analyze the combination treatment. Cells infected with JX-GFP showed an increased signal for PI in both cell lines, characterizing a more necrotic type of cell death (Figure  3A  and C ). The data of TG6002 infected cells were different in SK29-MEL-1 and SK29-MEL-1. 22. TG6002-infected SK29-MEL-1 cells showed the highest signal for late apoptosis (Figure  3D  and E ), SK29-MEL-1.
JX-GFP-infected cells did not show significant differences in the expression of calreticulin but even a lower expression of calreticulin. Cells treated with 5-FU alone displayed a higher expression of calreticulin. Aiming to study the expression of calreticulin at the point of cocultivation with DCs, flow cytometry was performed 7 d after treatment (48 h of viral infection following 5 d of 5-FC or 5-FU). Thus, a higher calreticulin expression, mostly described in early apoptosis of cells, might be measurable at earlier time points after viral infection. ATP levels were very low in all experimental settings (10 -8 mole ATP). There were no differences in ATP levels between the virally infected cells or the combination with 5-FC and 5-FU compared to untreated human melanoma cells (data not shown).
Acknowledgments Aspects of this article are part of the doctoral thesis of  J Klein ,  V Engel  and  L Geberzahn. The authors especially thank  Professor Dr PR Galle  ( First Department of Internal Medicine, University Medical Center Mainz ),  Dr CJ Breitbach  ( Sillajen Biotherapeutics ,  San Francisco ,  CA, USA)  and  P Schaefer  as outstanding technicians in our laboratory and for their contributions to the research.
Genomic prediction of hybrid performance We applied our resequencing data to carry out genomic selection to predict grain yield for test crosses. Four scenarios of prediction were investigated, namely the performance of grain yield in each of the three environments (control, early stress and late stress) and across environments. We observe high prediction accuracy, measured as the Pearson correlation coefficient between the predicted and observed values, standardized with the square root of the heritability (h = 0. 78), amounting to 0. 6 for the performance across environments. Analyses of this kind have been undertaken for grain yield in other crops using genomic selection  46. A modelling study recently found that with this level of prediction accuracy, genomic selection could substantially improve selection gain per year  47.
DISCUSSION Pearl millet is a staple food for more than 90 million people in Africa and Asia. People living in arid and semi-arid regions, in particular, rely on pearl millet, which can crop in the harsh conditions. We sequenced the genome of pearl millet reference genotype Tift 23D 2 B 1 -P1-P5 (available at https://www. ncbi. nlm. nih. gov/assembly/ GCA_002174835. 1/). The draft genome assembly presents 90% of the pearl millet genome with N50 of scaffolds as 884. 95 kb and 87. 2% assembled genome into seven pseudomolecules. The genome assembly of cereal species like pearl millet with high levels of repetitive DNA is always challenging. Therefore, in addition to a WGS approach, BAC-sequence data were used to develop the draft genome assembly and PacBio data were generated to validate the assembly.
With an objective to save the cost, but without losing information, 1. 68× coverage WGRS data and 0. 12× GBS data were generated on PMiGAP lines and 0. 59× coverage RAD-sequencing data were generated on B-and R-lines. The sequence information from the more genetically diverse PMiGAP inbred panel will be of broader use for genome-wide association mapping and allele mining. All of these sequences are available at https://www. ncbi. nlm. nih. gov//sra/?term= SRP063925. Resequencing data of almost 1,000 pearl millet lines (963 inbreds of cultivated pearl millet and 31 heterozygous wild individuals, available at https://www. ncbi. nlm. nih. gov// sra/?term=SRP063925) provides researchers and breeders with an enormous resource of genome-wide variations including SNPs, indels, SSRs and structural variations (Supplementary Tables  23 24 25 26 27 28 29 30 31 32 ) for mining alleles of genes with significant MTAs and for developing pearl millet hybrids with increased heterosis.
Development and improvement of genome assembly. For WGS assembly, clean reads were assembled by SOAPde novo 53 (Version 2. 04) (parameters: pregraph -s assembly. lib -K 63 -R -d 1 -o pm; contig -g pm -R; map -s assembly. lib -g pm -k 45; scaff -g pm). The k-mer frequency follows a Poisson distribution when read length << genome size  54. Short insert libraries were assembled into contigs. The reads were mapped back onto the contigs to estimate overlap between contigs. Gapcloser 53 (Version1. 10, parameter: -a pm. scafSeq. fill -b reads. lib -o pm. scafSeq. fillGap -t 24) within the SOAPde novo package was used to fill gaps in the scaffold with paired end reads. BAC-by-BAC sequencing of 100,608 BAC clones was conducted to improve the quality of the genome assembly. Each sequenced BAC was assembled separately by SOAPde novo.
1. 32  57. The TASSEL-GBS pipeline incurs an overhead for each separate pseudomolecule processed, hence we concatenated the thousands of individual scaffolds into ~20 megascaffolds to ease computation. Reads were processed into clean 64 bp "tags" and mapped against the reference scaffolds with Bowtie 2 (ref. 58). SNPs were called with the DiscoverySNPCallerPlugin in TASSEL, with minimal filters to reduce the number of false positives due to sequencing errors (minor allele frequency ≥ 0. 01, minor allele count ≥ 10, genotype calls in at least 10% of samples) (Supplementary Code 1). RAD sequencing. Genomic DNA of each B-and R-individual was digested with EcoRI. After electrophoresis, DNA fragments of the desired lengths were gel purified. Adaptor ligation and DNA cluster preparation were performed and fragments were sequenced on an Illumina HiSeq 2000 platform.