dataesr/scientific-paragraphs-categorization huggingface dataset:
Due to RFI in L-band, spws 0, 1, and 2 were flagged before all images were merged together into an image cube with the frequency as the third axis. This was done for the Stokes Q and U images separately. Then the script "RMsynth" (B. Adebahr, private communication, based on  Brentjens & de Bruyn (2005) ) was applied. A Fourier transformation was performed on the complex flux densities of the cubes in λ 2 -space. The result was a cube with the two image axes and Φ as the third axis. Then the RM of a single source along the line of sight was determined by fitting, for example, a parabola to the main peak of F(Φ)  (Brentjens & de Bruyn 2005). The result was a cube of Stokes Q and U, as well as a polarization cube, which was Fig. 1 : NGC 4666 Stokes I image of L-band combined (B-, C-, and D-configuration) with a robust zero weighting, overlayed onto the optical SDSS image made from the u, g, r filters.
Radio continuum Stokes I The total power map (Stokes I) of L-band is shown in Figure  1  with total intensity contours overlayed on the optical Sloan Digital Sky Survey (SDSS) 4  image made from the ugr filters using the formulas of Lupton 2005 5. The radio halo in the combined configuration of L-band (Figure  1 ) reaches up to 9 kpc above and below the plane of the galaxy as measured to the 3-σ level corrected for the beam size. The box-like appearance of the radio halo is quite striking. It is evident that the extent of the radio continuum radiation beyond the star-forming disk only occurs in the vertical direction of the galaxy. In Appendix A, we present L-band contours from the B-, C-, and D-configurations of the VLA, which result in different resolutions. The C-band data are presented in the following section.
Integrated spectral distribution The spectral index behavior of the integrated flux densities I of NGC 4666 is shown in Figure  2. Other integrated fluxdensity measurements from the literature were selected from the NASA/IPAC Extragalactic Database (NED) 6  and VizieR 7  , complementing the two CHANG-ES flux densities from this work (Table  6 ); only literature values with corresponding errors were used. The fitted spectral slope is α = -0. 68 ± 0. 04 (where I ∝ ν α ). This spectral index is typical for radio spectra with superposition of synchrotron and thermal radiation. The spectral index through the higher-frequency data shows hints of a steeper index. There is no indication of flattening towards the lower frequencies from the different GLEAM data.
These are comparable to Hα filaments emerging from the disk. With the new high-resolution CHANG-ES data this structure is now seen in the radio regime. Since the galaxy is classified as a superwind and starburst galaxy, these structures are probably best explained by a galactic wind from the disk and up into the halo. Therefore, the magnetic fields as well as the CRs are transported with the wind. This would result in advection being the main transport process of CRs, which agrees with what is found for this galaxy by  Heesen et al. (2018) ; this is further discussed in Section 3. 11. Similar filamentary radio structures described as threads were found in the center of the Milky Way by  LaRosa et al. (2000). The western and eastern side of the galaxy halo look very different in terms of this filamentary structure.
Further analysis of the XMM data Figure  4  shows the large-scale emission from the hot gas in NGC 4666. While the brightest emission comes from the central parts of the disk and the nuclear point-like source, the vertical outflows reach up to 9 kpc into the halo. The hot gas around NGC 4666 is also box-shaped as seen in radio. Interestingly, the bubble-like structure from the radio map coincides with a feature in the X-rays to the southeast. The spectral analysis was performed for three regions of NGC 4666: The central disk region was chosen to supplement the analysis of the magnetic fields of NGC 4666 in radio and has a boxsize of 140" × 28". Two additional regions of the same size on both sides of the disk region (east and west) were selected in order to look for possible changes in the energy budget of the ISM in the disk outskirts, as well as to study the emission for the hot gas in the galactic halo.
Scale heights The intensity profile perpendicular to the major axis of edgeon galaxies can be best fitted by exponential or Gaussian functions. We follow the scale height determination undertaken for 13 CHANG-ES galaxies in  Krause et al. (2018)  to fit twocomponent exponentials to the radio intensity profiles. The scale height analysis was carried out on the combined C-band and Lband data. To compare the results in both bands the maps were smoothed to the same beam size of 13. 3" × 13. 3". We used the "BoxModels" tool within the NOD3 software package  (Müller et al. 2017). The parameters of the analysis are presented in Table  13. For NGC 4666 it is not easy to find good fit solutions with two-component exponentials along the whole disk if the galaxy is divided into different strips along the major axis.
This model is used on the total intensity profile of the pure synchrotron maps, which represent the synchrotron intensity emitted by the CRe as well as on the corresponding spectral index map of NGC 4666. An interactive PYTHON wrapper around SPINNAKER (SPINTERACTIVE; Miskolczi 2018, private communication) was used to fit the data. 9 We varied the input parameters manually, while checking the quality of the fit on a graphical user interface, and thus arrived at the best-fitting solution. The main input parameter is the transport process, choosing between diffusion and advection. Depending on this choice, either the diffusion coefficient or the advection speed can be changed. Further parameters to be fitted are the CRe injection spectral index, γ 0 , the magnetic field strengths in total and of the thin disk component (B 0 , B 1 ), and magnetic field scale heights hb1 and hb2, for the thin and thick disk, respectively.
36 kpc. The results of RM synthesis show that NGC 4666 is characterized by an X-shaped large-scale magnetic field structure with an observed magnetic field reaching far into the halo. In C-band, the polarized intensity and magnetic field orientation were determined by imaging Stokes Q and U with a robust two weighting. In comparison to RM synthesis with robust two weighting, the polarization map from Stokes Q and Stokes U and robust two weighting shows 1. 2 times more polarized flux density. In the uv-tapered and smoothed images from archival VLA and from CHANG-ES data the large-scale X-shaped magnetic field in Cband is visible. In L-band, RM synthesis is useful and necessary to detect polarized intensity from the entire galaxy with a factor of 1. 4 of enhanced polarized flux density in comparison to imaging Stokes Q and U (both with robust two weighting).
Acknowledgements. We thank the anonymous referee for help in improving this work. We thank  B. Adebahr  for providing the RM synthesis scripts and  A. Basu  for detailed discussions and helpful suggestions. This research is kindly supported and funded by the  Hans-Böckler Foundation. This research was also supported and funded by the  DFG Research Unit   1254  " Magnetisation of Interstellar and Intergalactic Media: The Prospects of Low-Frequency Radio Observations ". The  National Radio Astronomy Observatory  is a facility of the National Science Foundation operated under cooperative agreement by  Associated Universities, Inc. We made use of the  NASA's Astrophysics Data System Bibliographic Services , and the  NASA/IPAC  Extragalactic Database (NED) which is operated by the  Jet Propulsion Laboratory, California Institute of Technology , under contract with the  National Aeronautics and Space Administration.
Genomes of powdery mildew fungi code for several hundred effector-like proteins: 491 Candidate Secreted Effector Proteins (CSEPs) were initially identified in the B. graminis f. sp. hordei genome  [4] , and it has become clear that there are even more in this f. sp. [5] , while 844 are currently described in the recently updated B. graminis f. sp. tritici genome  [6]. These putative effectors have a predicted amino-terminal signal peptide for secretion, lack recognisable transmembrane domains, and have no relevant BLAST hits outside of the powdery mildew family (Erysiphaceae). As for most other pathogen effectors, their mode of action is not yet understood. Previously, two complementary bioinformatic procedures were used to identify CSEPs with predicted RNA-binding or RNase folds: InterProScan combined with Gene Ontology characterisation, and IntFOLD, an integrated structure prediction server.
CSEP0064/BEC1054 shows structural similarity to T1 RNases To provide detailed insights into the molecular architecture of RALPH effectors, we determined the structure of CSEP0064/BEC1054 by X-ray crystallography. An initial model obtained from a dataset phased by iodide-SAD (single-wavelength anomalous diffraction) was subsequently used to calculate phases for a native dataset at 1. 3 Å via molecular replacement. Data processing and refinement statistics for the structures are outlined in S2 Table. Analysis using the Dali server  [24]  confirmed that CSEP0064/BEC1054 is a close structural homologue of T1 RNases, a family of enzymes with high degree of specificity for cleavage of substrates at the 3' end of guanosyl residues. The crystal structure reveals a canonical (α+β) fold comprising a core four-stranded anti-parallel β-sheet packed against an α-helix, and a second shorter peripheral anti-parallel β-sheet formed from the N-terminal hairpin and C-terminal strand β7 (Fig  3A ).
In the RNA profiles from CSEP0064/BEC1054 transgenic leaves processed in the same way, the area of this peak was reduced. Likewise, this peak was reduced or absent in RNA from CSEP0064/BEC1054 transgenic plant leaves extracted at eight days post inoculation with B. graminis f. sp. tritici or at five days after MeJa treatment. In the controls with no MeJA induction, the area of the peak was very small or not detectable (Fig  6A ). In sum, these data suggest that MeJa treatment triggers fragmentation of rRNA, which is indicated by the occurrence of a presumptive degradation product. This process appeared to be impeded by the presence of CSEP0064/BEC1054 or by powdery mildew infection. We then measured these effects quantitatively. The area of the peak representing the presumptive rRNA degradation product was determined, relative to the area of the small (18S) and large (28S) rRNAs.
75 numerical aperture water-immersion objective. Transformed cells were identified through observation of DsRED fluorescence, which was excited at 561 nm using the 560 nm diode laser. Fluorescence emission was detected between 600 and 640 nm using a photomultiplier tube detector. mYFP fluorescence was excited at 514 nm with an argon laser at 20% base power and 5% laser power for imaging. Fluorescence emission was detected between 520 and 540 nm using a HYD detector with 250 V gain for all images. Sequential imaging was conducted by 400 Hz scanning speed and 5x frame averaging. Image capture and analysis was performed using Leica SP8 software. Further editing was performed using FIJI software v2. 0  [77]. For semiquantitative assessment of BiFC signals, transformed cells were manually assigned to one of four categories: strong, medium weak or no detectable YFP fluorescence.
RNA extraction and analysis Total RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen). RNA was quantified with a NanoDrop-1000 spectrophotometer (Thermo Scientific). Aniline (1. 2 μl, 1 M)(�99. 5%, Sigma) was used to treat 10 μl, containing up to 1 μg of extracted RNA in RNase free water, and incubated in the dark at 60 o C for three minutes, following which 2 μl of 5 M ammonium acetate stop solution with 100 mM EDTA was added and the mixture transferred on ice. The RNA was then precipitated by adding ethanol (1 ml), incubated at -80 o C for 20 min, and then collected by centrifugation. The quantity of RNA recovered was measured (NanoDrop 1000) and then analysed using an Bioanalyzer RNA Nano 6000 kit (Bioanalyzer 2100, Agilent Technologies, Santa Clara, CA). The peaks of interest were indentified manually, and the areas under the peaks measured using the manucfacturer's software (Agilent Technologies 2100 Expert, 2009).
Crystallisation of CSEP0064/BEC1054 and structure solution Purified CSEP0064/BEC1054 was dialysed into crystallisation buffer (10 mM Tris, 150 mM NaCl, pH 7. 0) and concentrated to 10 mg/ml for crystallisation. A variety of commercially available solution conditions for crystallisation (Hampton Research,CA, USA) were screened using the sitting-drop vapour diffusion method. CSEP0064/BEC1054 was combined with the mother liquor on a 1:1 ratio in 200 nl drops. Crystals obtained in 0. 1 M sodium acetate buffer pH 5. 0, supplemented with 30% PEG 4000, 0. 4 M (NH 4 ) 2 SO 4 were cryoprotected with 30% glycerol and flash frozen for data collection. A native dataset to 1. 3 Å resolution was collected at a wavelength of 0. 92 Å using the I04 beamline (DIAMOND Light Source, Oxford, UK) and a second derivative dataset collected at a wavelength of 0.
95 Å (above the iodide f" edge) from crystals that had been soaked in mother liquor supplemented with 0. 5 M sodium iodide. Initial processing, scaling and structure factor calculation of native and iodide SAD datasets was performed using XDS  [83, 84]  and TRUNCATE  [85]  respectively, from within the XIA2 program  [86]. Phasing of the derivative dataset was performed via single-wavelength anomalous diffraction with density modification, using autoSHARP software (Global Phasing Ltd. , Cambridgeshire, UK)  [87]. Following calculation of protein phases, a partial model was built automatically in ARP/wARP  [88]. The model was extended through manual model-building in Coot  [89]. The refined CSEP0064/BEC1054 structure was thus used as a search model to phase the higher resolution native dataset via molecular replacement using Phaser MR  [90].
Iterative cycles of model building and reciprocal space refinement were performed in Coot  [89]  and Refmac5  [91] , respectively, until convergence of R work values, where 5% of reflections were excluded for cross-validation. Both models obtained from SAD and native datasets contained a single copy of CSEP0064/ BEC1054 in the asymmetric unit, and all residues were built with the exception of the N-terminal alanine, the side chain of R76 and the C-terminal G97, due to missing or ambiguous density in maps. Model validation was performed using tools in Molprobity (Chen, Arendell et al. , 2010).
Curve fitting was performed using the NTAnalysis software (Nanotemper Technologies) in the Thermophoresis + T-Jump mode for the SRL ligand, and using the Hill equation for the total RNA. K D values calculated using non-linear regression. For NMR experiments, CSEP0064/BEC1054 protein at a concentration of 50 μM was titrated with from 0. 5 to up to 80 M equivalents of a DNA SRL oligonucleotide sequence, where 2D 1 H 15 N HSQC spectra were recorded for each titration point as outlined. Experiments were performed in 50 mM Tris, 150 mM NaCl, at 308 K. Analysis of chemical shift perturbations was performed in CCPN Analysis  [93].
Statistical analyses Bartlett tests were performed for numerical datasets to determine whether the variance was homogeneous  [95]. General Linear Models (GLMs) were conducted on all datasets except for the infection of transgenic wheat with B. graminis f. sp. tritici, where a Generalised Linear Mixed Model (GLMM) was utilised. Where possible, model simplification was performed, and non-significant or non-interacting factors removed, resulting in the minimal model. For the GLMs, linear hypotheses were tested in a pairwise manner using Games-Howell post-hoc tests. The only assay in which a two-way interaction of factors was detected was the RNA extraction and analysis (described above). A GLMM was used, as non-normal repeated measures (i. e. the fact that the old and young leaves were from the same plants, and the different leaf sections used originated from the same leaves), can be accounted for through the addition of random effects  [95].
For the GLMM, the count data corresponding to the total number of germinated conidia (with and without functional haustoria) was bound as a single vector, creating the response variable "y". To take into account pseudoreplication (due to sampling repeatedly from the same plants/leaves), age, genotype and leaf segment were set as fixed effects, and a binomial family was used due to the response variable being count data. The linear hypotheses were investigated in a pairwise manner using the "multcomp" package in R. For the phenotyping assay, a "Poisson" family structure was used to account for count data, and datasets were logged to account for overdispersion in the original models (where the residual deviance is much greater than the degrees of freedom).
Accession numbers Sequence data from this article can be found in the EMBL/GenBank data libraries under the following accession number(s): 40S 16, accession KP293844; eEF1γ, accession KP293852; eEF1α(1) and eEF1α(3), accessions KP293845 and KP293846; GST, accession KP293847; MDH, accession KP293848; NDPK, accession KP293849; PR10, accession KP293851; CSEP0064/BEC1054, accession CCU83233. 1; CSEP0264, accession CCU83219. 1; and CSEP0102, accession CCU74258. 1. The structure of CSEP0064/BEC1054 is available in protein data bank (PDB) under accession number 6FMB.
This research was funded by the  Biotechnology and Biological Sciences Research Council-UK  ( BB/M000710/1 ) to PDS and ( BB/ K021435/1 ) to EJW, the  ERA-CAPS  project  DURESTrit  ( PA 861/13 ), and a project within the  Deutsche Forschungsgemeinschaft Priority Programme   SPP1819  ('Rapid evolutionary adaptation: Potential and constraints') to RP (PA.
TOB binding to alginate Calcium-alginate gels were formed by adding 200 µL of alginate solution at 2% m/v in Eppendorf tubes and then, after centrifugation, 600 µL of 0. 1M TRIS-HCl buffer pH 7 containing 0. 1M of CaCl2. After 4 hours of gelation, 550 µL of liquid was removed and 500 µL of TOB solution in TRIS-HCl was added. After incubation for 7 days at 37 °C, the free TOB concentration in the liquid phase in equilibrium with the gel was determined by the LC-MSMS method described below. A control without alginate gel was treated in the same conditions to evaluate the TOB stability and plastic tube binding. No significant change in TOB concentration was observed in the control over the 7 days. The data for three experiments on binding of TOB to calcium-alginate gel were analyzed as described by Nichols et al.
RNA extraction and reverse transcription quantitative PCR (RT-qPCR) RNA was extracted from leaf samples using the RNeasy Plant Mini Kit (Qiagen, UK). cDNA was synthesized using 1 µg of RNA using the QuantiTect Reverse Transcription Kit (Qiagen). Reverse transcription quantitative PCR (RT-qPCR) in the presence of SYBR Green was carried out using a BioScript PCR kit (Bioline, UK) according to the manufacturer's instructions in a Rotor-Gene 6000 apparatus (Corbert Life Science, Australia). All the data was normalized to housekeeping genes (ACTIN and/or UBIQUITIN) and the calculated efficiency was added to the analysis. Primer sequences are summarised in Supplemental. Table  S3. All reactions were carried out in triplicate.
Image and flow cytometry analysis, determining cellular parameters of leaf samples To visualize the leaf or cotyledon epidermis, a gel cast was made of the leaf surface, specifically the adaxial side of the first leaf pair, which was then observed under a DIC light microscope Nikon Optiphot 2 as described  (Horiguchi et al. , 2006). First true leaf pairs of WT and of various transgenic lines were dissected from seedlings at 8 or 12 DAG. Leaves were stained with propidium iodide (PI, 20 mg/ml) and images on the abaxial side of three different zones (the basal, middle and tip part) of the leaf were taken and analyzed by confocal laser microscopy (Leica SP5, Germany). Across the three zones, approximately 600 cells were counted and measured per leaf sample, n≥3 were studied for each transgenic line and the control using the Image J software.
Average cell size was calculated and the total cell number was extrapolated to the whole leaf according to previously described methods  (Asl et al. , 2011). The stomata number and stomatal index was calculated in a similar way. For determining the circularity of epidermal cells by using Image J software, guard cells were extracted  (Andriankaja et al. , 2012). To visualize the distributions of the cell area, only non-guard epidermal cells from the three zones were pooled together and used for calculation at a given time point, unless described otherwise  (Asl et al. , 2011). The number of elongated pavement cells with newly formed cell wall (described as extra cell division) was counted in all three zones and extrapolated to the whole leaf. For flow cytometry measurements, the first leaf pairs were collected and chopped with razor blades in nuclei extraction buffer and stained with DAPI as described before  (Magyar et al.
Acknowledgements We thank  Ferhan Ayaydin  ( BRC Szeged, Hungary ) for helping in microscopy, and  Anita Kovács  ( BRC Szeged, Hungary ) for her assistance in plant work. E. Ő. ,  A. P-Sz , T. L. , E. M. and Z. M. were supported by the  Hungarian Scientific Research Fund  ( OTKA K-105816 ) and by the  Ministry for National Economy  (Hungary,  GINOP-2. 3. 2-15-2016-00001 ). T. L. was funded by the  Young Scientist Fellowship  of the  Hungarian Academy of Sciences ,  A. P-Sz. was supported by the  GINOP-2. 3. 2-15-2016-00032. Cs. P and B. M. H. were funded by the  Marie Curie IEF fellowships  ( FP7-PEOPLE-2012-IEF. 330713  and  FP7-PEOPLE-2012-IEF. 330789 , respectively). Cs. P. and L. B were funded by the  BBSRC-NSF  grant ( BB/M025047/1 ). The funders had no role in the design of the study, data collection and analysis, decision to publish, or preparation of the manuscript.
were supported by the  Hungarian Scientific Research Fund  ( OTKA K-105816 ) and by the  Ministry for National Economy  (Hungary,  GINOP-2. 3. 2-15-2016-00001 ). T. L. was funded by the  Young Scientist Fellowship  of the  Hungarian Academy of Sciences ,  A. P-Sz. was supported by the  GINOP-2. 3. 2-15-2016-00032. Cs. P and B. M. H. were funded by the  Marie Curie IEF fellowships  ( FP7-PEOPLE-2012-IEF. 330713 and  FP7-PEOPLE-2012-IEF. 330789 , respectively). Cs. P. and L. B were funded by the  BBSRC-NSF  grant ( BB/M025047/1 ). The funders had no role in the design of the study, data collection and analysis, decision to publish, or preparation of the manuscript.
5 ). Though noting that single sensor operation is what rendered the earlier magnetic surveys of Giddings and Anderson unusable (the differential measurement of the gradient would likely have solved their problems with background noise  (Urban, 2012 )), we have found that as long as appropriate base station corrections are undertaken (with logged data) and inappropriate survey times are avoided (e. g. noisiest times of the solar day; predicted magnetic storms), then single sensor operation is wholly suitable for hearth detection at high latitudes. General instrument and survey parameters are listed in Table  2. Data editing and diurnal trend removal (in cases where base stations were used) were done using MagMap 2000 © , and data gridding done using Surfer 14 ®. Plan view mages were produced with Surfer 14 ® and 3-D images incorporating magnetic and ground-penetrating radar data were produced with Voxler 4 ® , both by Golden Software Inc.
Acknowledgements The work presented in this paper was sponsored by multiple sources, including several  Cooperative Ecosystem Study Unit (CESU) agreements between Cornell University  and the  U. S. Department of the Interior  as well as a  National Center for Preservation Technology and Training (NCPTT)  grant ( NPS-P15AP00094 ) also awarded to Cornell, and other direct support from the  U. S. National Park Service. Other support came from the  National Science Foundation : Kobuk Valley  was funded by  NSF  awards  0908162  and  0908462.