dataesr/scientific-paragraphs-categorization huggingface dataset:
2014). De novo assemblies were conducted with CLC Genomics Workbench 7. 0 (CLCbio, Aarhus, Denmark) using default settings. Mitochondrial protein-coding and rRNA gene sequences of all published annelids were used as tblastn queries to search for mitochondrial fragments in the Sa. spallanzanii assembly. The top-hitting contig identified by BLASTN recovered the entire mitochondrial genome of Sa. spallanzanii. The final contig was annotated using MITOS server under the mitochondrial code for invertebrate mitochondria  (Bernt et al. 2013) , including the protein coding genes and the secondary structure of tRNAs and rRNAs. Gene boundaries generated from automatic annotations were manually examined and adjusted, and the tRNAs identified by MITOS were rechecked via the tRNAscan-SE web server  (Schattner et al.
2005). Amino-acid sequences of protein-coding genes of 14 annelids belonging to Sedentaria (as selected by  Tilic et al. (2020b)  from available mitochondrial genomes), including M. occidentalis, and an outgroup Marphysa sanguinea  (Montagu 1813)  belonging to Errantia, were used for phylogenetic analysis. Sequences were aligned using Muscle  (Edgar 2004 ), implemented in Geneious 2020. 0. 5. The concatenated matrix was partitioned by gene. The best fitting evolutionary model for each partition was selected and the maximum likelihood analysis was performed in IQ-TREE 1. 3. 4 (Nguyen et al. 2015). Bootstrap support was estimated using an ultrafast bootstrap algorithm (UFBoot)  (Minh et al. 2013 ) for 1000 replicates. The mitochondrial genome of Sa. spallanzanii (GenBank accession number MW002660), length 15,581 bp, is AT-rich (64.
Funding This work was supported by the  French State in the frame of the "Investments for the future" Programme IdEx Bordeaux  under Grant  ANR-10-IDEX-03-02  ( Guillemine Daffe );  Australian Biological Resource Survey (ABRS)  under Grants  RF213-19  and  RG18-21 , and  Australian Museum Foundation  grant ( Elena Kupriyanova  and  Shane T. Ahyong ).
1 (Gamma) variant, which eludes the human immune response to the ancestral variant that was prevalent earlier in 2020. 3 imilar immune evasion of B. 1. 351 (also known as the Beta variant of concern) was also described in South Africa and has led to a major second wave. 4 Similar to these two countries, high seroprevalence was not sufficient to prevent Madagascar from having a second major peak in early 2021. Introductions of Beta in the country were first detected in early February, 2021 (GISAID accession IDs EPI_ISL_1660263, _1660266, _1660268, _1660270, _1660272-75, _1660278-79, _1660283-84 and _1660286-290), but the degree to which this variant contributed to the last epidemic wave remains unclear. In 2020-21, we continuously monitored natural immunisation of the population of Antananarivo by sampling the city's blood donors from the Regional Blood Transfusion Centre in Antananarivo, as previously described 1 (from Oct 1, 2020, to May 26, 2021; mean of 421•9 samples per month, 3375 total samples; appendix p 3).
The low variability in phosphate concentration contrasted with that of alkaline phosphatase activity, which varied over 1 order of magnitude across the transect. Nanomolar phosphate data revealed gradients of phosphate concentration over density inside the PDL ranging between 10. 6 ± 2. 2 µmol kg -1 in the westernmost station to values close to zero towards the east. Using the density gradients, we estimated diapycnal fluxes of phosphate to the PDL and compared them to atmospheric deposition, another external source of phosphate to the PDL. Phosphate supply to the PDL from dry deposition and diapycnal fluxes was comparable in the western part of the transect. This result contrasts with the longtime idea that, under stratification conditions, the upper waters of the Mediterranean Sea receive new P almost exclusively from the atmosphere.
, Ocean Data View, https://odv. awi. de/, last access: 6 September 2021, 2021). As described in Sect. 2 (Material and methods), phosphate vertical profiles were built up from two datasets: one with phosphate concentration obtained through standard technique, with a limit of quantification of 0. 02 µM (red line), and another one with phosphate concentration below 0. 02 µM, obtained through the nanomolar LWCC technique. water samples were spiked with 100 µL of MUF-P solution diluted so that different concentrations (0. 025-1 µM) were dispatched into a black 24-well polystyrene plate in duplicate. Incubations were run in the dark in thermostated incubators reproducing in situ temperature and lasted up to 24 h with a measurement of fluorescence every 1-3 h depending on expected activities. The rate was calculated from the linear part of the fluorescence versus time relationship.
The wet deposition P fluxes were estimated from the measured dissolved concentrations in the rain samples multiplied by the total precipitation accumulated during the period of the rain over the R/V location  (Desboeufs et al. , 2021). The total precipitation during the rain events was estimated from the hourly total precipitation accumulated on the grid point encompassing the R/V position from ERA5 data reanalysis. The accumulated rate was 3. 5 ± 1. 2 mm at ION and 5. 7 ± 1. 4 mm at FAST.
, 2011 ; Pasqueron de Fom-   2 , and plots from short stations can be found in Fig. S1. Vertical gray lines mark the threshold between the nanomolar and micromolar phosphate dataset (phosphate concentration = 20 nM). mervault et al. , 2015). However, except for a few studies  (Moutin et al. , 2002; Thingstad et al. , 2005; Pulido-Villena et al. , 2010; Djaoudi et al. , 2018a) , phosphate concentrations measured above the phosphacline (i. e. , inside the phosphate-depleted layer) were below the detection limit of standard methods used, precluding the assessment of vertical and regional variability of this key phosphate pool. Surface nanomolar phosphate data obtained in this study fall within the same order of magnitude as previously reported values for the open Mediterranean Sea during the stratification period by  Van Wambeke et al.
, 2017). It should be noted that dry deposition data were derived from measurements of total soluble phosphorus including inorganic and organic fractions. Given the potential high contribution of the organic fraction to total soluble phosphorus in atmospheric deposition (e. g. ,  Djaoudi et al. , 2018b) , phosphate fluxes from dry deposition were likely overestimated. The occurrence of rain events significantly enhanced the contribution of atmospheric deposition to new P supply to the surface layer. This was particularly the case at FAST due to the occurrence of a Saharan dust event  (Guieu et al. , 2020b)  with an estimated dust flux between 38 and 55 mg m -2 , mainly through wet deposition  (Bressac et al. , 2021; Desboeufs et al. , 2021). Diapycnal fluxes and atmospheric deposition represent an external supply of new phosphate to the surface layer between 0.
Contribution of regenerated phosphate to total P requirements Dissolved organic phosphorus represents an alternative source of P in P-depleted oceanic regions  (Hoppe, 2003 , Mather et al. , 2008). In this study, the combination of nanomolar phosphate data and alkaline phosphatase (AP) activity showed an enhanced utilization of DOP, particularly at the more oligotrophic stations located towards the east of the transect. It should be noted here that DOP hydrolysis in this study was assessed solely through alkaline phosphatase activity and was, therefore, restricted to phosphate monoesters. Other organic P compounds such as phosphate diesters or phosphonates are known to provide alternative sources of P  (Dyhrman et al. , 2006; Whitney and Lomas, 2019; Thomson et al. , 2020). A variable fraction of DOP is actually available for hydrolysis by alkaline phosphatase (hereafter AP-DOP).
Conclusions This study presents the first cross-basin dataset in the Mediterranean Sea based on collocated measurements of phosphate pools at the nanomolar level (phosphate, DOP, POP), alkaline phosphatase activities and atmospheric deposition of soluble/dissolved P. Microbial phosphorus cycling in the surface layer showed a marked longitudinal gradient despite little variability in phosphate concentration. Nanomolar phosphate measured at high vertical resolution inside the phosphate-depleted layer revealed vertical gradients between the surface and the phosphacline, challeng-ing the traditional view of a homogeneous phosphate deplete layer with phosphate concentration below the detection limit of measurement. Gradients of phosphate concentration versus density inside the PDL allowed estimating diapycnal fluxes of phosphate to the mixed layer and comparing them with another external source, atmospheric fluxes.
Data availability. Underlying research data are being used by researcher participants of the PEACETIME campaign to prepare other papers, and therefore data are not publicly accessible at the time of publication. "Biogeochemical dataset collected during the PEACETIME cruise"  (Guieu et al. , 2020a)  will be accessible at https://www. seanoe. org/data/00645/75747/. Supplement. The supplement related to this article is available online at: https://doi. org/10. 5194/bg-18-5871-2021-supplement. Author contributions. CG and KDe designed the cruise strategy. KDe was responsible for the collection and analysis of atmospheric deposition assisted by FF and ST. KDj measured nanomolar phosphate on board. FVW measured alkaline phosphatase activity assisted by SG. VT managed CTD operations on board. SB, AD, AP and VT contributed to the calculation of diapycnal fluxes.
SN managed phosphate sampling and analysis through standard techniques. TG analyzed DOP concentration. EPV supervised the nanomolar phosphate data and managed the analysis of the dataset. EPV wrote the manuscript with contributions from CG, KDe, KDj, FVW, SB, AD, AP and VT. Competing interests. The contact author has declared that neither they nor their co-authors have any competing interests. Disclaimer. Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Special issue statement. This article is part of the special issue "Atmospheric deposition in the low-nutrient-low-chlorophyll (LNLC) ocean: effects on marine life today and in the future (ACP/BG interjournal SI)". It is not associated with a conference.
Acknowledgements. This study is a contribution of the  PEACE - TIME  project (http://peacetime-project. org, last access: 7 April 2021), a joint initiative of the MERMEX and ChArMEx components. PEACETIME was endorsed as a process study by  GEO-TRACES  and is also a contribution to the IMBER and SOLAS international programs. We thank the captain and crew of the RV Pourquoi Pas? for their help during the work at sea. We also warmly thank  Fabrizio D'Ortenzio  for his insightful comments on the first version of the manuscript. The constructive comments during the review process of  Maurizio Ribera d'Alcalà , an anonymous referee,  Silvia Becaglis  and  Christine Klass  are much appreciated. Financial support. The project leading to this publication received funding from  CNRS-INSU ,  IFREMER ,  CEA  and  Météo-France  as part of the program MISTRALS coordinated by  INSU  and from the  European FEDER  fund (grant no.
The antennas were set up such that the electric field polarization was oriented across track, above a single sheet of plywood for stiffness and thin PVC mat for slipperiness. Data were collected at travel speeds of 2-3. 5 m s -1 over the course of a week in November and December 2019. Data processing consisted of coherent integration (i. e. , unfocused SAR), pulse compression, motion compensation (by tracking internal horizons), coherent channel combination, and de-speckling using a median filter. Two-way travel time was converted to depth assuming a correction of 10 m of firn air and a constant radar wave speed in ice of 168. 5 m µs -1 (e. g. ,  Winter et al. , 2017). After other processing was complete, different radargrams were spliced together to create a continuous profile extending from EDC to BELDC, and then the data were interpolated to have constant 10 m horizontal spacing.
5 Myr old ice, though the lack of stratigraphy does not allow firm conclusions regarding the We are thankful for the thoughtful comments from reviewers Lucas Beem and Xianbin Cui, from Marie Cavitte, and from editor Joe MacGregor, which improved the manuscript. Financial support. This research has been supported by the Horizon 2020 (Beyond EPICA (grant no. 815384)), the National Science Foundation (grant no. 1921418), and the Villum Foundation (grant no. 16572). Review statement. This paper was edited by Joseph MacGregor and reviewed by Lucas Beem and Xiangbin Cui.
extent to which useful climatic information may or may not be preserved below 2565 m depth. by national partners and funding agencies in Belgium, Denmark, France, Germany, Italy, Norway, Sweden, Switzerland, the Netherlands, and the United Kingdom. Logistical support is mainly provided by PNRA and IPEV through the Concordia Station system. The radar shipment and personnel transportation to Antarctica were provided by the US NSF under grant 1921418, which also partly supported the development of the VHF radar. Radar development was further supported by internal funding from the University of Alabama. David A. Lilien and Dorthe Dahl-Jensen were partially supported by the Villum Foundation (grant number 16572). The opinions expressed and arguments employed herein do not necessarily reflect the official views of the European Union funding agency or other national funding bodies.
Micromagnetic Simulations: The Mumax3 software package  [67]  was used to perform the micromagnetic simulations and the unit cell size was set to 2 × 2 × 1 nm  3. The material parameters were as follows: saturation magnetization M s = 8. 0 × 10 4 A m -1 , exchange stiffness constant A = 5. 0 × 10 -12 J m -1 and uniaxial magnetocrystalline anisotropy K u = 5 × 10 3 J m -3. To simulate the CSL with an asymmetric DM interaction, only the DM interaction in the x direction (helical axis) D x was considered and was set to ±3. 0 mJ m -2 for the right/ left-handed CSL. The corresponding L-TEM contrast patterns were simulated using the MALTS code via the Aharonov-Bohm expression. [68, 69].
Acknowledgements C. Z. , J. Z. , and C. L. contributed equally to this work. This work was financially supported by  King Abdullah University of Science and Technology (KAUST) ,  Office of Sponsored Research (OSR)  under the Award Nos. CRF-2018-3717-CRG7  and  CRF-2019-4081-CRG8. This work used the resources of the  Supercomputing Laboratory at KAUST. Y. P. and J. Z. would like to thank the funding support from the  National Natural Science Foundation of China  ( 51771085 ,  51571104 ,  51801087 , and 91962212). Z. Q. Q. acknowledges the support from  US Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division  under Contract No. DE-AC02-05CH11231  ( van der Waals heterostructures program ,  KCWF16 ).
Two East Asian Lomariopsis (Lomariopsidaceae, Polypodiales) species, Lomariopsis moorei and Lomariopsis longini, which were previously misidentified as L. spectabilis, are here described as new species based on evidence from morphological characters and a molecular phylogeny. The two species differ from the three other described species in East Asia by their venation, pinna shapes, and perine morphology. A phylogeny based on a combined dataset of three chloroplast regions (rbcL+ rps4-trnS + trnL-L-F) showed that L. moorei and L. longini each formed a well-supported monophyletic group which was distantly related to both L. spectabilis and the other morphologically similar East Asian species, L. boninensis.
1994 ) and 1379R  (Pryer et al. 2001)  for rbcL. PCR amplifications were prepared in 15 μL reactions each containing 20 ng of genomic DNA, 1× SuperRed PCR Master Mix RED (TOOLS, Newtaipei City, Taiwan) and 0. 5 μM of each primer. A typical amplification program began with one initial denaturation step for 5 min at 94 °C then 35 cycles of 1 min at 94 °C, 30 s at 55 °C, and 1 min at 72 °C followed by a final extension of 10 min at 72 °C and was performed on a SimpliAmp Thermal Cycler. PCR products were cleaned using ExoSAP-IT (Thermo Fisher Scientific, Waltham, Massachusetts, USA), and then sequenced with the same PCR primers with an ABI 3730XL (Thermo Fisher Scientific, Waltham, Massachusetts, USA) by the Genomics BioSci. & Tech. company in Taiwan. GenBank accession numbers of the sequences are listed in Appendix 1.
Acknowledgements We thank  Cheng-Wei Chen ,  Dirk Nikolaus Karger  ,  Yi-Han Chang ,  Ran Wei ,  Leon Perrie ,  Joel Nitta ,  Jinmei Lu , and  Wei-Hsiu Wu  for collecting DNA materials for this study;  Fay-Wei Li  for generating the DNA sequences of Lomariopsis sorbifolia;  Alexandria Quinlan  for English edits;  Robbin Moran ,  Tom A. Ranker , and  Blanca León  for the comments on the manuscript revision. The staff in herbaria KUN, P, TAIF, and TNS are gratefully acknowledged for the loan of specimens. The  MNHN (Paris, France ) gives access to the collections in the framework of the  RECOLNAT national Research Infrastructure. This project was supported by  MOST  project ( 109-2621-B-007-001-MY3 ) in Taiwan, the  Bioresource Conservation Research Center in College of Life Science  from the Higher Education Sprout Project by  MOE ,  Biodiversity Information Fund for Asia project  ( BIFA6_010 ), and  Mr.
0. 0. 2 (Agena Biosciences). The assay was performed on the genomic DNA extracted from 95 samples of L. sarmentosa collected in the NW Mediterranean (Table  1 ), using the DNeasy Blood and Tissue kits from QIAGEN. Allele calling was carried out with Typer Viewer v. 4. 0. 24. 71 (Agena Biosciences). Monomorphic SNPs, loci with weak or ambiguous signal (i. e. , displaying more than three clusters of genotypes or unclear cluster delimitation) and loci with too much missing data were all discarded. The genetic parameters, including observed heterozygosity, expected heterozygosity, and the Hardy-Weinberg equilibrium (HWE), were calculated using GenoDive 2. 0b23  (Meirmans and van Tienderen 2004).
Acknowledgements This work was funded by the  Agence de l'Eau Rhône-Méditerranée-Corse  under project  ICONE -Impacts actuels et potentiels de la CONnectivité Ecologique ajoutée par les récifs artificiels sur la biodiversité fixée des substrats durs du Golfe du Lion  (PI,  K. Guizien ,  AAP 2016 ). The authors gratefully acknowledge the helpful assistance during sampling of  S. Blouet  and the staff of the  Aire Marine Protégée Agatoise. We also thank the scuba divers,  JC Roca  and  B Hesse , for their technical assistance for field sampling in Banyuls sur Mer. We are grateful to the  Bio2Mar core facility  (http:// bio2m ar. obs-banyu ls. fr) for providing access to instrumentation for RNA extractions. RNAseq was performed at the  GeT-PlaGe core facility ,  INRAE Toulouse. SNP genotyping was performed at the  Genome Transcriptome Facility of Bordeaux  (grants from  ANR-10-EQPX-16 ) with the help of Laure Dubois.
Bioinformatic Analyses The bioinformatics analyses were performed using the USEARCH software following the UPARSE pipeline  (Edgar, 2013). The sequences were first trimmed to 250 bp, forward and reverse reads were merged and primers were removed. Quality filtering was performed using a maximum expected error threshold of 0. 5. After dereplication and singleton removal the sequences were clustered into operational taxonomic units (OTUs) based on 97% similarity using the UPARSE-OTU algorithm  (Edgar, 2013)  yielding 810 OTUs in total. The original reads were then mapped to the OTUs with the identity threshold of 0. 97. The sequence counts of all samples (abundances matrixes) were normalized by random subsampling to the minimal number of reads per sample (2,986 sequences, rarefaction) to avoid potential artifacts due to library size and lower the false discovery rates  (Weiss et al.
, 2017). We calculated rarefied OTU accumulation curves ("vegan" R package;  Oksanen et al. , 2020)  to explore the completeness of our sampling. While rarefaction curves indicated that additional sequencing depth would yield additional taxa in most samples, depth was relatively balanced among the treatments (Supplementary Figure  1A ), so unlikely to bias the abundance patterns after subsampling to a common read number. The OTUs were taxonomically assigned by comparing representative sequences to the UNITE database  (Kõljalg et al. , 2015)  (release date 01. 08. 2015), using the BLAST algorithm with default settings. The OTUs were assigned to particular taxa by selecting the hits with the lowest E-value and with a minimum alignment length of 75 bp. OTUs were subsequently assigned to functional groups if their genus was successfully matched with one of the genera whose trophic type have been described in  Tedersoo et al.
The proportion of unassigned OTUs may have had some contribution on the lack of unequivocal signs of competition between ectomycorrhizal and saprotrophic fungi. The proportion of unassigned OTUs was higher in Trenched plots (Supplementary Figure  3 , P = 0. 003), which most likely belong to saprotrophic fungi, since EcM fungi are fairly well-known and well-represented in the DNA databases. Nonetheless, our data do not show a clear deceleration of decomposition rates in presence of EcM fungi. The litter-derived CO 2 fluxes per unit of litter C did not differ significantly between Trenched (without EcM fungi) and Non-Trenched plots (with EcM fungi) (Figure  8c ). If any, the inhibiting effect of EcM fungi on litter decomposition rates was very low to be detected in this case, considering that lower levels of soil moisture in presence of roots (Table  4 ; Figure  7d ) may have also contributed to underestimate the litter-associated excess CO 2 flux in Non-Trenched plots.
DATA AVAILABILITY STATEMENT The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found at: Sequence Read Archive (SRA, http://www. ncbi. nlm. nih. gov/bioproject/747155, BioProject ID PRJNA74715). Data on soil variables and CO 2 fluxes are archived and publicly available at the online archives of the Helmholtz Centre for Environmental Research GmbH -UFZ (https://www. ufz. de/record/dmp/archive/7013/de/ and https:// www. ufz. de/record/dmp/archive/7016/de/, respectively).
The other group is synthetic insecticides such as organophosphates, pyrethroids, neonicotinoids, organochlorides, carbamates, ryanoids, and spinosyns. By 2021, more than 600 arthropod species have been included in the arthropod pesticide resistance database (https://www. pesticideresistance. org/) (accessed on 21 January 2021). Several genetic mechanisms of Bt resistance have been reported (reviewed in  [2] ). If a mutation in a midgut receptor causes reduced physical binding with Bt proteins, the toxicity of Bt can be decreased. These receptors include cadherin, aminopeptidase-N, alkaline phosphatases, and ATP-binding cassette transporters. Alternatively, altered processing of Bt prototoxin, increased immune status, sequestration of Bt protein, and accelerated recovery of epithelial integrity can also increase Bt resistance.
Resequencing Data Resequencing data generated in our previous study were reused  [31, 33]. More specifically, this dataset included 29 sfC and 49 sfR individuals from invasive populations (Benin, Malawi, Uganda, China, and India) and 70 sfC and 29 sfR individuals from native populations (Mississippi, Florida, Puerto Rico, Brazil, French Guinea, Guadeloupe, and Mexico) (Figure  1 ) (please see Table  S1  for more information). This dataset includes four Bt-resistant and six susceptible Brazilian individuals. Paired-end whole genome resequencing was performed with approximately 20X coverage with 300 bp insert size, and 150 bp read length using Illumina (San Diego, CA, USA) HiSeq 2500, HiSeq 4000, and Novaseq 6000. Variant calling was performed using the GATK-4. 0. 11. 0 package  [35]  for single nucleotide variant (SNV) and CNVCaller  [36]  for copy number variation (CNV).