dataesr/scientific-paragraphs-categorization huggingface dataset:
Both datasets were remapped at 100 km resolution, enough to resolve the broader oceanographic scales of variability. In Particulate organic carbon. Water is filtered through Whatman 25 mm GF/F glass-fiber filters (filtered volume from 2. 27 to 5. 5 L, depending on samples). Filters were washed beforehand using the soxhlet extraction method with dichloromethane. After filtration, samples were put into petri dishes and stored in liquid nitrogen for the duration of the cruise and then transferred into -80 • C freezer until analysis, which took place within 12 months from sampling. Two days before the analysis, the filters were stored in a drying chamber at 50 • C during 1 night and then decarbonated with HCl solution. Finally, the filters were analyzed using a carbon, hydrogen and nitrogen (CHN) analyzer (Perkin Elmer 2400 series II) with the combustion analysis method.
Ocean Colour Data The full ESA OC-CCI v3. 0 (European Space Agency Ocean Colour-Climate Change Initiative version 3. 0) monthly TChla (mg m -3 ) and b bp (m -1 ; 443nm) data time-series at 4 km resolution for the period 1997-2015 over the global ocean was downloaded from the ESA-CCI website (http: //www. esa-oceancolour-cci. org/). ESA-CCI products are the results of the merging between SeaWiFS, MERIS, MODIS-Aqua, and VIIRS time-series  [25, [36] [37] [38]. TChla was estimated with a blending of the OCI (as implemented by NASA, itself a combination of CI and OC4), the OC5 (NASA, 2010) and the OC3 algorithms (http://www. esa-oceancolour-cci. org/?q=webfm_send/684). The Quasi-Analytical Algorithm (QAA) was used to compute b bp  [39, 40]. The accuracy of the QAA algorithm was demonstrated in several recent studies  [12, 13, 19, [23] [24] [25] 41].
If one focuses on the relationship between TChla and bbp, the goal being their comparison, the SMA (or RMA) has to be applied because it is statistically more robust in the context of the analysis of field measurements as explained in Section 2. 1. To further underline the difference in results when applying OLS or SMA methods, we computed the total Cphyto from Equation (2) and by using the bbp(700) 0-400 m profiles collected during the BOUSSOLE cruises. To each profile, we applied the b k bp(700) values (i. e. , intercepts) obtained after the application of both OLS and SMA methods (Figure  2 ). The RPD on Cphyto estimation is equal to 23. 5% (overestimation of total Cphyto using SMA instead of the appropriate OLS method). Additionally, in order to evaluate how the estimate of Cphyto changes when using either methods, we applied the relationships reported in Figure  2  to the time series of bbp(700) vertical profiles from the BGC-Argo dataset.
5 (±0. 2) × 10 -4 m -1 (with the OLS method), a value consistent with the order of magnitude found by a recent work always based on ocean colour data  [13]. With the SMA, the b k bp becomes lower with As discussed before, the definition of cause (independent variable) and effect (dependent variable) is thus fundamental and represents the working hypothesis. If one focuses on the relationship between TChla and b bp , the goal being their comparison, the SMA (or RMA) has to be applied because it is statistically more robust in the context of the analysis of field measurements as explained in Section 2. 1. To further underline the difference in results when applying OLS or SMA methods, we computed the total C phyto from Equation (2) and by using the b bp (700) 0-400 m profiles collected during the BOUSSOLE cruises.
To each profile, we applied the b k bp (700) values (i. e. , intercepts) obtained after the application of both OLS and SMA methods (Figure  2 ). The RPD on C phyto estimation is equal to 23. 5% (overestimation of total C phyto using SMA instead of the appropriate OLS method). Additionally, in order to evaluate how the estimate of C phyto changes when using either methods, we applied the relationships reported in Figure  2  to the time series of b bp (700) vertical profiles from the BGC-Argo dataset. When assessing the integral of C phyto over depth and time, the RPD between C phyto,SMA and C phyto,OLS is 28. 7%. In this example, the use of SMA (the less adapted method) leads to an overestimation of C phyto. Furthermore, we conducted the analysis by using 19-years of monthly ocean colour data of TChla and b bp (443) for the period 1997-2015 as shown in Figure  3.
Funding: The  BOUSSOLE  project is co-funded by the  European Space Agency (ESA)  and  Centre Nationales d'Etudes Spatiales CNES; France). This study was also supported by the following research projects: remOcean (funded by the  European Research Council , grant agreement  246777 ), NAOS (funded by the  Agence Nationale de la Recherche  in the frame of the  French "Equipement d'avenir" program , grant agreement  ANR   J11R107-F ). M. B. conceived this work during his stays at the  Laboratoire d'Oceanographie de Villefranche sur Mer (LOV)  supported by a postdoctoral fellowship of the (CNES; France). Currently, M. B. has a postdoctoral fellowship by the  ESA. This work was supported by the  ESA Living Planet  Fellowship Project PHYSIOGLOB: Assessing the inter-annual physiological response of phytoplankton to global warming using long-term satellite observations,  2018-2020.
Results phylogenetic analysis of methionine synthase in haptophytes. A survey of methionine synthase isoforms in 19 haptophyte species based on transcriptomic and genomic datasets has been conducted (see Supplementary Table  1  on Supplementary Information for sequences details). All samples investigated contained the B 12 -dependent metH. The phylogeny of this phylum was reconstructed from this gene, with species from orders Coccolithales, Isochrysidales and Prymnesiales relevantly gathered (Fig. 2 ). This reconstruction was consistent with what is usually found for 18S sequence  31  , suggesting an absence of horizontal gene transfer. The cobalamin-independent isoform metE was not found in any of the samples, indicating that all 19 species are B 12 -auxotrophic (Fig. 2 ). The Marine Atlas of Tara Ocean Unigenes (MATOU) for eukaryotic data  32  was also investigated by searching similar genomic and proteomic sequences of METE from Phaeodactylum tricornutum and Chlamydomonas reinhardtii.
The MATOU database gather large-scale environmental metatranscriptomic and metagenomic information. Since no haptophyte sequence was retrieved in these large datasets, this reinforces the hypothesis of absence of B 12 -independent methionine synthase in the haptophyte lineage. Considering that comprehensive genomic and transcriptomic data of Tisochrysis lutea (Isochrysidaceae) were available, it was taken as model species for molecular physiology analyses depending on cobalamin quotas. In silico searches in T. lutea (strain CCAP 927/14) genome  31, 33  allowed to identify several genes involved in vitamin B 12 metabolism, conversion and transport. Gene metH coding for cobalamin-dependent methionine synthase was found and the presence of the related protein was confirmed in our proteomic dataset.
The expression of methionine cycle genes and mmcm did not show a clear trend (Fig. 5A-C ,F; Supplementary Dataset 1; Supplementary Fig. 2  in Supplementary Information). In comparison, genes cblA and cblB were significantly repressed (p = 0. 02 and p = 0. 04; two-tailed Student's t test) by 72-fold and 11-fold respectively (Supplementary Dataset 1; Supplementary Fig. 2 ). This finding suggests that B 12 starvation decreases expression of genes involved in cobalamin transport and conversion. It must be pointed out that growth rate decrease at the end of the batch culture may lead to cellular processes influencing many biochemical pools. Therefore, the expression of genes analyzed here may be the result of a global physiological state not specifically related to B 12 starvation. A more accurate approach using cobalamin-limited chemostat was thus undertaken to confirm the effect of different vitamin B 12 status on genes expression.
Molecular analyses. Genes expression analyses were carried out on samples collected at each physiological state to relate genes expression patterns to nutrient quotas. Genes for which expression was followed were the same as those of the batch experiment. Results presented for steady-state correspond to the third sample collected, just before nutrient spike. As can be seen in Fig. 7G , at steady-state all genes involved in methionine cycle were more expressed in B 12 limitation than in nitrogen limitation by 4-fold (metH) and 8-fold (metK and sahH) (Fig. 7G ; Supplementary Dataset 2 and Supplementary Fig. 4  in Supplementary Information). Genes cblA and cblB were around 2-fold less expressed in cobalamin limitation than in nitrogen limitation, whereas mmcm was expressed almost at the same level (Fig.
Discussion Haptophytes microalgae play an important role in carbon  17, 18  and sulphur cycling  20  but their ability to respond to cobalamin variations is poorly known, despite the previously described impact of B 12 limitation on phytoplankton growth and community composition  2, 3, 35. The aim of this work was to (1) analyze B 12 dependency of haptophytes based on molecular data and (2) provide insights into cobalamin molecular physiology of haptophytes by studying the model marine microalgae Tisochrysis lutea. This work combined bioinformatic searches, growth tests in batch and chemostat at different levels of B 12 availability with the analyses of cobalamin quotas and expression of genes involved in B 12 metabolism. Nineteen haptophyte species across six orders and nine families were assessed for the presence of methionine synthase isoforms.
All species investigated encoded the B 12 -dependent metH only. It has been observed that cobalamin auxotrophy is determined by the presence of metH and the absence of the cobalamin-independent methionine synthase metE  11, 12. Our results, mainly based on transcriptomic datasets, suggest that all of these haptophytes are cobalamin auxotrophs. No metE sequence of haptophytes was retrieved from the MATOU database, supporting the idea that species of this phylum are B 12 -requiring for growth. On the other hand, Croft et al. 11  reported the occurrence of 8 haptophyte species among the 22 analyzed that did not require cobalamin  11. It must be pointed out that 2 species over 22 were grown in their study and the remaining 20 were compiled from literature without any information about bacterial contamination.
Also, the reaction of MMCM is one of many entries in TCA cycle and there could be other mechanisms of regulation at this metabolic level which could explain the lack of modifications in mmcm expression. In the proteomic dataset from the N-limited chemostat described by Garnier et al. 39  , methionine cycle proteins and MMCM belonged to the top 400 highest accumulated proteins over the 4330 identified during steady-state. Proteins CBLA and CBLB were not detected in their experiment  39. In general, our expression analysis trends are in accordance with their proteomic results, as genes cblA and cblB were the lowest expressed. To our knowledge, this is the first time that an analysis of B 12 molecular physiology of a microalgae has been conducted in chemostat with accurately described nutrient states.
lutea and related to oxidative stress response, triacylglycerol synthesis and photosynthesis  41. Genes cblA and cblB were found to belong to a same group regulated by a shared transcription factor but methionine cycle genes were not gathered in a same module  41. McRose et al. 42  identified riboswitches affiliated with genes overexpressed in thiamine (vitamin B 1 ) starvation in haptophytes microalgae  42. Therefore, it is likely that such regulation mechanism would play a role in regulating, directly or not, cobalamin-related genes. In conclusion, this is the first time that B 12 dependency of haptophytes has been investigated. Based on 19 species surveyed, and since no haptophyte from the MATOU database was found encoding cobalamin-independent methionine synthase, we propose that haptophytes are cobalamin auxotrophs.
Searches for methionine synthase isoforms in other haptophytes were firstly realized by BlastX of T. lutea METH on NCBI database, allowing to retrieve METH from Chrysochromulina sp. CCMP 291, Thalassiosira pseudonana CCMP 1335 and Phaeodactylum tricornutum CCAP 1055/1. The iMicrobe database was then queried, yielding sixteen haptophyte transcriptomes samples corresponding to 9 haptophyte families (see Table  1  in Supplementary Material for sequence references). TblastN of METE from C. reinhardtii (XP_001702934. 1, NCBI) and P. tricornutum (B7G1X4, Uniprot); and METH from T. lutea were realized on the transcriptomes. Transcripts were translated into proteins using NCBI ORFfinder. Protein sequences were then aligned with METH from T. lutea and T. pseudonana and METE of P. tricornutum. Protein sequences were also verified by sequences alignments and conserved domains analyses.
Identity and similarity with T. lutea sequences were estimated with LALIGN tool. Sequences alignment was conducted with MUSCLE (full mode) on the 21 METH sequences with T. pseudonana and P. tricornutum taken as outgroup. On total, 1206 positions were conserved on the 1508 initial (80%). Curation step was done with Gblocks tool, allowing gap positions within the final blocks and phylogenetic tree was realized with PhyML (100 bootstraps). Sequences homologous to genomic and proteic METE from P. tricornutum and C. reinhardtii were searched in the Marine Atlas of Tara Ocean Unigenes (MATOU) for eukaryotic data  32  using BlastP and TBlastN (expected threshold 1E-1). Algal strain and purification. To limit bacterial contamination, a purification step was carried out on Tisochrysis lutea CCAP 927/14 strain with an antibiotic treatment mix prepared following the method described by Cho et al.
Six genes coding for 18S, actin, EF1, GAPDH, tubulin and ubiquitin were tested as housekeeping genes. As GAPDH exhibited low cycle threshold (Ct) variations with the same order of magnitude than target genes it has been selected as reference gene (see Fig. 1  of Supplementary Information). Gene expression was calculated by raising negative cycle threshold values of each pair of primers and dividing it by mean expression of reference gene. Raw data of genes expression is available in Supplementary Datasets 1 and 2 for the batch and chemostat experiments respectively.
Acknowledgements This work was supported by the  Atlantic MIcroalgae program  consortium funded by  Région Pays de la Loire. The authors wish to thank  Ewa Lukomska  for dedicated assistance for carbon and nitrogen measurements,  Jean-Baptiste Bérard  for kind help and support during the chemostat experiment,  Bruno Saint-Jean  and  Gaël Bougaran  for kind assistance and helpful comments on the results.
Aims. NGC 4631 is an interacting galaxy that exhibits one of the largest, gaseous halos observed among edge-on galaxies. We aim to examine the synchrotron and cosmic-ray propagation properties of its disk and halo emission with new radio continuum data. Methods. Radio continuum observations of NGC 4631 were performed with the Karl G. Jansky Very Large Array at C-band (5. 99 GHz) in the C and D array configurations, and at L-band (1. 57 GHz) in the B, C, and D array configurations. Complementary observations of NGC 4631 with the Effelsberg telescope were performed at 1. 42 and 4. 85 GHz. The interferometric total intensity data were combined with the single-dish Effelsberg data in order to recover the missing large-scale total power emission. The thermal and nonthermal components of the total radio emission were separated by estimating the thermal contribution through the extinctioncorrected Hα emission.
In this paper we present observations of NGC 4631 with the Karl. G. Jansky Very Large Array (VLA) at C-band and Lband (Sect. 2. 1) and with the Effelsberg telescope at 1. 42 and 4. 85 GHz (Sect. 2. 2). The single-dish and interferometric data were combined in total power (Sect. 2. 4). Results for total power (TP), thermal and nonthermal separation, vertical scale heights, and spectral indices of NGC 4631 are presented in Sect. 3. This is followed by a discussion in Sect. 4 and conclusions in Sect. 5. The parameters of NGC 4631 assumed in this study are presented in Table  1. In all radio maps presented in this paper, the beam area is shown as a filled circle in the left-hand corner of each image.
Observations and data reduction 2. 1. VLA data at C-band (5. 99 GHz) and  Radio polarimetric observations of NGC 4631 were performed with the Karl G. Jansky Very Large Array (VLA) during its commissioning phase through the project Continuum HAlos in Nearby Galaxies -an EVLA Survey (CHANG-ES). The CHANG-ES project is a survey of 35 edge-on galaxies that exploits the new wide-band capabilities of the VLA  (Irwin et al. 2012a (Irwin et al. ,b, 2013;; Wiegert et al. 2015; Irwin et al. 2015; Li et al. Notes. (a) IR center at 2. 2 µm  (Irwin et al. 2011 ). (b) From this paper, see Sect. 3. 5. (c) We assume an average position angle of 85 • along the major axis. (d) From  Seth et al. (2005) , determined from the tip of the red giant branch method. -An angular size of 1 corresponds to 2. 2 kpc. 2016;  Damas-Segovia et al.
2016; Irwin et al. 2017; Krause et al. 2018; Vargas et al. 2018 ). The data were taken at C-band (5. 0 -7. 0 GHz) in C and D array configuration, and at L-band (1. 25 -1. 50 and 1. 65 -1. 90 GHz) in the B, C, and D array configurations. Details of the observations are summarized in Table  2. The primary calibrator 3C286 was used to determine the bandpass and the absolute polarization angle. To calibrate the instrumental polarization leakage, one scan was carried out on the unpolarized source OQ208 (J1407+2827). For the observation at C-band in the D array configuration the secondary calibrator J1310+3220 was used as a polarization leakage calibrator due to its wide range in parallactic angle (> 60 • ). Due to the relatively small size of the primary beam in the C-band observations, which has a full width at half maximum (FWHM) of ≈ 7.
5 as compared to the angular extent of NGC 4631 of 15 , we performed observations with two pointings to cover the entire galaxy. The pointings were placed on each side of the center along the disk of the galaxy separated by 3. 75. At L-band, the FWHM of the primary beam is about 30 , hence, one pointing was sufficient. Total intensity and polarization calibration, as well as imaging of the data, were performed using the Common Astronomy Software Applications (CASA;  McMullin et al. 2007 ) package as described in detail in  Irwin et al. (2013)  and  Wiegert et al. (2015). The data were imaged using the MS-MFS algorithm  (Rau & Cornwell 2011). All datasets were self-calibrated once in both amplitude and phase, verifying that the model to be used for self-calibration did not include any artifacts or any extended negative components.
The self-calibration table made with the Stokes I image was then applied to the Stokes Q and U data. For all images, the Briggs' robust weighting scheme  (Briggs 1995)  was used (robust = 0 for all Stokes I images). In order to emphasize broad-scale structures at lower resolution in the Stokes I images, we utilized the u,v taper option within the cleaning algorithm. By combining datasets in different array configurations we improved the u,v coverage, the signal-to-noise ratio, and the spatial dynamic range. At C-band, both pointings were self-calibrated and imaged separately. Consequently, the primary beam (PB) correction was applied on each of the corresponding Stokes I pointings and both images were combined as described in  Wiegert et al. (2015) (Sect. 3. 3. 5). We refer to the companion paper  Mora-Partiarroyo et al.
(2019)  for results and analysis concerning the polarization data (hereafter denoted as Paper II). The Effelsberg data were reduced with the new NOD3 software package  (Müller et al. 2017) , with which scanning effects due to weather conditions, receiver instabilities, and radio frequency interferences (RFIs) were removed. The scans of the galaxy at each observing frequency were combined and flux density calibration was done by using 3C 286. We assume the 3C 286 flux density scale as measured by the NRAO 1. The zerolevels of the maps were corrected accordingly. At 4. 85 GHz, the angular resolution of the map is 163 FWHM and the rms noise is 580 µJy/beam in total intensity and 140 µJy/beam in polarized intensity. The resulting total power emission is plotted in Figure  1. At 1. 42 GHz the angular resolution is 561 FWHM and the rms noise is 33 mJy/beam in total intensity.
( e) The flux densities in the 4. 85 GHz Effelsberg map published by  Mora & Krause (2013)  were underestimated, because the smaller size of their scanned area made it difficult to estimate an accurate baselevel. The flux densities presented in Table  3  indicate that the VLA data at both frequencies suffer from missing spacings even in the most compact D-configuration. Therefore, single-dish data need to be combined with the VLA data to recover the missing flux   (8, 12, 24, 48, 96, 192, 288). The background radio galaxy to the southwest of NGC 4631 has been marked with a black X-symbol (see Appendix A). density attributed to the incomplete u,v coverage of the interferometer. The spectrum of the integrated emission is discussed in Sect. 3. 3.
Merging strategy The Effelsberg and the VLA total intensity maps were merged in the image plane with the new NOD3 algorithm "ImMerge"  (Müller et al. 2017). This algorithm combines both maps by first creating a map of the difference of the interferometric map (smoothed to the resolution of the single-dish beam) from the single-dish map. This map is then rescaled by the ratio of the two beams (VLA beam/Effelsberg beam) and, consequently, added to the interferometric map at its original resolution. By combining the Effelsberg and VLA maps we recovered about 34% at C-band and 12% at L-band of the total flux density of the galaxy, which is attributed to the large-scale structures. All of the total intensity images presented in Sect. 3 were obtained by combining Effelsberg and VLA data with the NOD3 algorithm.
In Table  4  we have summarized the rms values of the merged maps at all the various resolutions presented in this paper. To compare the merging procedure, we also tested combining the single-dish and interferometric data with the Astronomical Image Processing System (AIPS) task "IMERG" and the CASA task "feather". We obtain a similar result with the feather and ImMerge tasks, while with IMERG the emission of the galaxy is more extended in the northeastern and southwestern quadrants giving NGC 4631 a more asymmetric appearance. Since most edge-on galaxies studied up to now reveal a rather symmetric distribution of the radio halo emission  (Wiegert et al. 2015) , we believe that the ImMerge NOD3 algorithm and the feather CASA task are more accurate in this respect for our NGC 4631 data.
Spectrum of the integrated radio continuum emission To study the radio continuum spectrum of NGC 4631, we use only integrated flux densities obtained from single-dish telescopes (Table  3 ). Extrapolation of the thermal flux density determined in Sect. 3. 2 to 1. 0 GHz yields 73±14 mJy and a thermal fraction of 4. 0±0. 9%, which is smaller by a factor of 3. 5±0. 8 compared to the value of 14±1% obtained by fitting the spectrum of total emission by a nonthermal component with a spectral cutoff plus a thermal component  (Klein et al. 2018). This large discrepancy cannot be explained by the uncertainties of our method of measuring the thermal emission. We suspect that the quality of the spectral data of NGC 4631 is not sufficient to reliably measure the thermal fraction and the cutoff frequency independently from the radio spectrum alone.