dataesr/scientific-paragraphs-categorization huggingface dataset:
For quantification of WB and IP assays, films were scanned and, if appropriate, subjected to band densitometry and quantification using Image J software (RRID:SCR_002285). Each band value was normalized according to the background of the filter and its loading control. The appropriate sample size ('n') was determined based on previous experiments of identical characteristics from our previous publications  (Andersen et al. ; Urban et al. )  and similar published data from other groups, using a minimum of 3 mice per condition for in vivo experiments, and a minimum of triplicate for in vitro experiments. Throughout this paper, 'technical replicate' refers to the same sample being tested multiple times; 'biological replicate' refers to independent biological samples. All data collected were included, as variation was considered within expected ranges and variances were non-significant.
Statistical analyses were conducted using the GraphPad Prism seven software (RRID:SCR_002798) using a two-sample unpaired t test assuming Gaussian distribution for the comparison of two conditions; paired t test was used for Figure  4E-I,L-N , where the control and treatment conditions for each biological replicate were performed on cultures in parallel; or ordinary one-way ANOVA followed by Tukey's multiple comparisons test, for the pairwise comparison of three conditions. All error bars represent the mean ± SEM. Significance is stated as follows: p>0. 05 (ns), p<0. 05 (*), p<0. 01 (**), p<0. 001 (***), p<0. 0001 (****), confidence intervals of 95%. Statistical details of each experiment can be found in the figure legend. n represents number of independent biological repeats.
Acknowledgements We gratefully acknowledge  Lan Chen  for technical support,  Rekha Subramaniams  and  Nicholas Chisholm  for managing the mouse colony, the  Advanced Sequencing Facility, Bioinformatics and Biostatistics Facility, Experimental Histopathology Facility and Flow Cytometry Facility of the Francis Crick Institute  for their help and support,  Jane Johnson ,  Ryoichiro Kageyama ,  Ana Lasorella ,  Randall Reed ,  Jane Visvader  for providing mice,  Gilbert Rahme ,  Matthew Havrda  and  Mark Israel  for plasmids,  Hiyaa Ghosh  for advice on Tcf4 immunostaining,  Runrui Zhang  and  Verdon Taylor  for sharing data and manuscript before publication and members of the  Guillemot lab  for discussions. NU was supported by a fellowship from the  Francis Crick Institute  and is currently supported by  IMBA (Austrian Academy of Science ); BR was supported by  H2020-MSCA-IF-2014 ; DvdB was supported by a  Marie Curie Fellowship , project  799214 ; EH was supported by  Ligue Nationale contre le Cancer, Fondation ARC  pour la recherche sur le cancer (PJA 20131200481, PJA 20151203259) and  FP7 Marie Curie CIG.
Means of the OECD's biosafety work: • harmonisation of approaches and regulatory frameworks; and • share/disseminate common base of scientific information. He explained that the main outputs of the OECD's work on biosafety could take the form of: (a) exchange or cooperation meetings, conferences or workshops, during which biosafety authorities of the OECD member countries and its guest members discussed current and upcoming issues, (b) ''consensus'' and guidance documents that helped national assessment and decision-making processes, and that represented practical tools for comparing conventional and ''genetically engineered'' products, 3  and (c) a database on transgenic products that had been approved for release in the environment and/or food and feed use. 4 earns also alerted the audience to a previous workshop, organised by the OECD Working Party on Biotechnology, Nanotechnology and Converging Technologies (BNCT), held on the 29-30 September 2016 in Ottawa, Canada.
Reconstruction of genomic sequences from the main bacterial population of the seed microbiome. Competition for nutritional resources between phytopathogenic agents and other members of the seed microbiome was subsequently estimated with genomic sequences. Given the limited number of fungal reads in our metagenomics datasets, we restricted this comparative genomic analysis to bacterial populations and Xcc8004. Bacterial genomic sequences were either recovered through metagenomic read sets or via genome sequencing of representative bacterial isolates (see materials and methods). Overall, 11 metagenomeassembled genomes (MAGs; >50% completeness, <10% contamination) and 21 genomes sequences were obtained (Table  1 ). These genomic sequences represented the major bacterial species detected with the ParaKraken taxonomic classification approach, and, based on their gyrB sequences, represented the main gyrB amplicon sequences variants (ASVs) of the radish seed microbiomes (Table  1  and Additional file 6  24, 35  ).
DISCUSSION Microbial interactions occurring on and around the seed are important for plant fitness, since seed-borne microorganisms are the primary source of inoculum for the plant. Depending on the outcome of the interactions, these microbial assemblages could either promote or reduce plant growth  9. Understanding the processes involved in the assembly and resilience of the seed microbiota is especially relevant to comprehend the emergence of plant diseases. In the current work we assessed whether niche preemption occurred during seed-transmission of two phytopathogenic agents, Xcc8004 and Abra43, which differ in their transmission modes. According to our metagenomic datasets, the radish seed microbiome was mostly composed of eubacteria. Whether this estimation reflects the actual structure of the radish seed microbiome or represents a bias due to DNA extraction/classification methods is currently unknown.
Taxonomic inference of metagenomics reads The relative abundances of Xcc8004 and Abra43 within seed samples were estimated by mapping metagenomic reads to their respective genome sequences  23, 58. Taxonomic profiling of each metagenome was estimated with a modified parallel version of Kraken  59  , named ParaKraken  33  , creating a count table of species and a relative abundance for each sample. Reads affiliated with the species Xanthomonas campestris and Alternaria brassicicola were removed in the count table for richness and diversity analyses (see Text S1 for details). Richness and diversity were calculated with the R package phyloseq 1. 22. 3  60 on species count table. Differences in observed richness, estimated richness and diversity between samples were assessed through Kruskal-Wallis non parametric analysis of variance followed by Dunn's post-hoc test.
Differences in community membership and composition were estimated with the Jaccard and Bray-Curtis index. Principal coordinate analysis (PCoA) was used for ordination of Jaccard and Bray-Curtis distances. A permutational multivariate analysis of variance (PERMANOVA) was carried out to assess the impact of pathogen transmission on seed-associated microbial community profiles. To quantify the contribution of the seed transmission of phytopathogenic microorganisms on microbial community profiles, a canonical analysis of principal coordinates (CAP) was performed with the function capscale of the R package vegan 2. 4. 2, followed by PERMANOVA with the function adonis. OG DUO networks were split into a network of positive interactions and negative interactions and then clustered using MCL  67  to identify groups of highly interconnected OGs.
Reconstruction of metagenome-assembled genomes Initial binning was performed with Metabat v. 0. 32. 4  68. Metagenome-assembled genomes completeness, contamination and strain heterogeneity were evaluated with CheckM v 1. 0. 4  69. Taxonomic affiliation of each bin was performed by Average Nucleotide Identity based on BLAST (ANIb) with Jspecies  70. Closest ANIb values were selected for reference genomes and used for Circle Packing representation with the D3. js JavaScript library representation (see details in Text S1).
Community profiling of germinating seeds and radish seedlings Seed samples harvested in plot X2014 were used to determine the dynamics of bacterial population during germination and emergence of radish. DNA extraction and subsequent gyrB amplicon library preparation were performed on germinating seed (n=6) and seedling (n=8) samples according to the procedure described earlier  46  (see details in Text S1). Libraries were sequenced with a MiSeq reagent kit v2 (500 cycles). Fastq files were processed with DADA2 1. 6 73 using the parameters described in the workflow for "Big Data: Paired-end". The only modification made regarding this protocol was a change in the truncLen argument according to the quality of the sequencing run. Species abundance was assessed on germinating seed and seedling samples with the R package phyloseq  60  (ASVs taxonomic affiliation details in Text S1).
Acknowledgements The authors wish to thank  Guillaume Chesneau  for his help with bacterial competition assays,  Laurent Noel  for providing the strain pTac::GUS-GFP, the FNAMS for running field experiments, the  ANAN platform (SFR QuaSav)  for amplicon sequencing and  BGI  for sequencing the bacterial genomes. We would also like to thank  BBRIC network  for all the bioinformatic support.
Funding This research was supported by the grant awarded by the  Region des Pays de la Loire  (metaSEED, 2013 10080);  RFI Objectif Végétal (DynaSeedBiome)  and the  AgreenSkills+ fellowship programme , which has received funding from the  EU's Seventh Framework Programme  under grant agreement n°  FP7-609398. This research used resources from the  Oak Ridge Leadership Computing Facility  at the  Oak Ridge National Laboratory , which is supported by the  Office of Science of the U. S. Department of Energy  under Contract No. DE-AC05-00OR22725. This research was also supported by the Plant-Microbe Interfaces.
Jones (2017) has also explored how agricultural biodiversity, diet quality and anthropometric outcomes are associated in LI and LMI countries. A comprehensive review of five databases revealed that agricultural biodiversity has a small but consistent link with more diverse household and individual diets, although the magnitude of this association varies with the extent of the existing diversification of farms. Greater richness in on-farm crop species is also associated with small, positive increments in linear stature in young children. Agricultural diversification may contribute to diversified diets through both subsistence and income-generating pathways and may be an important strategy for improving diets and nutrition outcomes in LI and LMI countries.
In vivo imaging Albino C57BL/6 mice were used for in vivo imaging studies. Mice that were previously fed the different diets for 8-weeks were infected with 10 4 PFU MAYV expressing nLuc in the hind left footpad. Following infection, mice were monitored for viremia and luminescence. Mice anesthetized with ketamine/xylazine were intraperitoneally injected with furimazine (20 μg/mouse, a gift of Yves Janin, Institut Pasteur) and imaged within 5 minutes of furimazine administration for 15 seconds. Photon flux (photons/second) was quantified using Living Image software (Perkin-Elmer). All images contained at least one uninfected control animal. For data analysis, we selected the hind left footpad as the region of interest (ROI). We then normalized the flux values within the ROI of each infected mouse to the flux of the ROI of the uninfected mouse present in the same image.
For comparisons between extracted and unextracted samples for qRT-PCR, data were compared using a twotailed paired t-test. All experiments were repeated 2-3 times unless otherwise noted. The data are presented as the result of one representative experiment. To further assess nutritional status, we measured serum levels of the adipokine leptin. Leptin, a pro-inflammatory adipokine primarily secreted by adipocytes, is a blood marker that generally increases during obesity and decreases in severe undernourishment  [45]. Obese mice had significantly increased levels of leptin in their serum following 8-10 weeks of feeding compared to lean controls (Fig 1B  , p<0. 0001). Leptin levels in LP mice were not significantly different from controls (p = 0. 2935).
9863 for the obese and LP groups compared to lean controls, respectively). To assess the infection rate of the mosquitoes fed on individual mice, we first analyzed the data by measuring infection and transmission rates from each mouse. Mosquitoes that fed on obese mice had reduced infection and transmission rates compared to lean controls (Fig 7B  and 7C , p = 0. 0451 and 0. 0443, respectively). The infection and transmission rates observed in LP and control groups were not significantly different. The infection rates for obese mice varied from 6. 3-55%, LP from 15-50%, and lean controls from 35-75%. The transmission rates for obese mice varied from 0-5%, LP from 0-20%, and lean controls from 5-15%. 60% and 20% of obese and LP mice had no mosquitoes found to be transmission positive following feeding, whereas all the lean controls resulted in transmission positive mosquitoes.
Acknowledgments We are incredibly grateful to  Yannis Michalakis  and  Renaud Vitalis  for their stimulating discussions on genetic bottlenecks and thorough review of the manuscript. We thank  Brandy Russell  at the  CDC  for providing the virus strains used in these studies. We are grateful to  Andrew Routh  for his kind assistance with data analysis. We would also like to acknowledge  Janet Webster  for her thoughtful review of the manuscript. We much appreciate  Yves Janin ,  Jean-Pierre Levraud , and  Gabriella Passoni  for their collaborations and enjoyable discussions. Finally, we are indebted to the animal care technicians and other technical staff at the  Pasteur Institute , without whom this work would not have been possible.
| OCP and crevice corrosion testing The stabilized OCP of the tested alloys was measured as a function of DOC in natural seawater. Titanium (grade 2) wires were used for electrical contact allowing OCP measurements. OCP was measured with high impedance (>10 11 Ω) data loggers connected to a gel reference electrode Ag/AgCl/KCl. The electrodes were calibrated weekly with a certified SCE. The criterion for stabilized potential was arbitrarily fixed to no potential evolution of more than ±5 mV over 48 hr (after a minimum exposure time of 15 days). Continuously renewed seawater (from the Bay of Brest, France) was used to allow a continuous supply of bacteria and nutrient from the natural seawater. The temperature was controlled at 30. 0 ± 0. 5°C (regulated by heating bands) and the renewal rate was about one complete renewal per day of the seawater in the cells (i.
The V4-V5 region of the 16S ribosomal RNA (rRNA) bacterial marker gene was amplified by a polymerase chain reaction (PCR) with the 518F and 926R primers fused with Illumina adapters and sample-specific sets of barcodes and indexes. PCR products were visualized on agarose gels and purified with AMPure XP (Agencourt) reagent. DNA concentrations were assessed with Quant-iT™ Pico-Green® double-stranded DNA (Invitrogen) before pooling the PCR products at equimolar concentration. Sequencing using Illumina MiSeq platform was performed at the Josephine Bay Paul Center (Woods Hole, MA). Sequences were deposited into the European Nucleotide Archive under the accession number PRJEB30977 (http://www. ebi. ac. uk/ena/data/view/PRJEB30977).
| Bioinformatic analysis of the DNA The quality filtering of raw sequencing data was carried out following the recommendations of Minoche et al. (2011),  [22]  while merging paired-end reads with Illumina-Utils python scripts on demultiplexed raw reads. [23] We then performed operational taxonomic unit (OTU) delineation with the Swarm algorithm, which uses a local linking threshold (default, d = 1) for sequence clustering and internal abundance structure to break chained OTUs. [24] We used VSEARCH  [25]  to detect and remove chimeras, and the Silva NR 128  [26]  database for taxonomic assignment of Swarm representative sequences with mothur. [27] tacked bar plots were produced with ggplot2. [28] We used the two conditions "stainless steel with oxygen" and "glass with oxygen" to perform biomarker detection with LEfSe.
2013 (Fisher et al. , 2016)). Analysis of the complete lidar dataset shows that the entire malpaís landform of 26 km 2 is covered with architectural features of varying densities  (Fisher et al. 2017). The most intensively occupied portions are distinct monumental zones distributed throughout the malpaís. This multinucleated settlement is unusual for Mesoamerica  (Mastache et al. 2008; Sanders et al. 2003)  and potentially for the Purépecha Empire  (Pollard 2003). This also means that Angamuco is an example of an urban landscape similar to what has been observed at Cantona and the Malpaís of Zacapu (e. g. ,  Cook and Carrión 1998; Forest 2017; Millon 1973). We have documented more than 60 distinctive, standardized, and recurrent architectural forms throughout the site, including commoner and elite buildings, altars, pyramids, storage facilities, ball courts, and a hierarchical road system.
Architecure at Angamuco An initial version of the architectural typology described here was created in 2007 for a fullcoverage survey on the former island of Apúpato (Pezzutti 2010). It included a data dictionary with drop-down menus that was then entered into a relational database. The typology was updated and expanded in 2009 for the initial season of mapping/survey at Angamuco and was incrementally modified in subsequent years to reflect the types of features encountered at the site (for early versions, see  Ahrens 2013; Bush 2012; Cohen 2016; Fisher, Bush et al. 2011; Urquhart 2015). The 2010 version was printed, laminated, and carried in the field by trained archaeologists as a quick reference. Thousands of ancient buildings and associated landscape features are visible on the surface of Angamuco.
E. Smith 2011). The increasing use of lidar, computer modeling, and other techniques that are ushering in new preservation methods is facilitating such approaches  (Fernandez-Diaz et al. 2018; Llobera 2011). To achieve comparative goals and to analyze big data, archaeologists must new find ways to categorize, quantify, and analyze large and varied types of qualitative and quantitative data. Our field sample is one way to apply computational analysis to a large site using lidar data. Using such datasets, we can understand more about the urban layout of sites that are not always well preserved. Although modern construction and erosion will always be a problem for archaeologists, a bird's-eye urban map can help. We are just scratching the surface of Angamuco research, and this typology forms the foundation for ongoing and future work at the site.
Acknowledgments. This analysis was supported by grants to  Chris Fisher  from the  National Science Foundation  ( BCS 0818662 ,  BCS 1220016 ), the  National Geographic Society , the  NASA   Space Archaeology Program , and  Colorado State University. We thank the  Fontezuelas community , the  Tzintzuntzan municipal government , the  Tzintzuntzan Community Heritage Council ,  INAH-Michoacán , and the  LORE-LPB  field crews between 2009 and 2014 for their help. We appreciate the comments of three anonymous reviewers, which have improved this article.
Bioinformatics analysis Bacterial and plant sequences were identified in the databases by BLASTP and TBLASTN. Alignments were constructed with T-Coffe implemented in the Macvector package. Targeting prediction were tested using the SUBA web site (http://suba. plantenergy. uwa. edu. au) Phylogenetic trees were built with PhyML v3. 1 (www. phylogeny. fr) using the neighbor-joining method implemented in the BioNJ program. Graphical representations were performed with TreeDyn (v198. 3). The Arabidopsis RADA structure was modeled on the structure of RadA from Streptococcus pneumoniae (pdb: 5LKM), using Modeller (http://salilab. org/modeller/about_modeller. html). For Illumina sequence analysis of the cpDNA, reads were aligned against the Arabidopsis reference genomes using Burrows-Wheeler Aligner (BWA)  (Li et Durbin, 2009)  and filtered to keep only those mapping to the cpDNA.
The coverage was extracted with Bedtool genomecov  (Quinlan et Hall, 2010)  and coverage positions were rounded down to the upper kb and the coverage of each 1 kb-range was normalized relative to 1,000,000 total Arabidopsis reads. For analysis of rearranged sequences, reads properly pairing to the cpDNA were filtered to only keep those showing a short-clipping sequence (threshold 20 nucleotides) and no indel (looking for the presence of a S in the CIGAR string without any I,D and H). The short-clipping sequences were then extracted with SE-MEI/extractSoftclipped (github. com/dpryan79/SE-MEI) and aligned using bowtie2  (Langmead et Salzberg, 2012)  against the cpDNA. The positions of the shortclipping sequences mapping the cpDNA and of their relative read were rounded down to the upper kb to analyse the localization of the rearrangement.
qPCR Analysis qPCR experiments were performed in a LightCycler480 (Roche) in a total volume of 6 µL containing 0. 5 mM of each specific primer and 3 µl of SYBR Green I Master Mix (Roche Applied Science). The second derivative maximum method was used to determine Cp values and PCR efficiencies were determined using LinRegPCR software (http://LinRegPCR. nl). Three technical replicates were performed for each experiment. Results of qPCR and RT-qPCR analysis were standardized as previously described  (Wallet et al. , 2015). The recently corrected Arabidopsis Col-0 mtDNA sequence was taken as reference  (Sloan et al. , 2018). Quantification of mtDNA and cpDNA copy numbers used a set of primer pairs located along the organellar genomes, as described previously (Le  Ret et al. , 2018; Wallet et al.
Flow cytometry and EdU staining Nuclear DNA content was measured in leaves of 20-d-old seedlings, using the CyStain UV Precise P Kit (Partec) according to the manufacturer's instructions. Nuclei were released in nuclei extraction buffer (Partec) by chopping with a razor blade, stained with 4',6-diamidino-2-phenylindole (DAPI) buffer and filtered through a 30 µM Celltrics mesh (Partec). Between 20,000 and 30,000 isolated nuclei were used for each ploidy level measurement using the Attune Cytometer and the Attune Cytometer software (Life Technologies). At least four independent biological replicates were analyzed. EdU staining was as described  (Pedroza-Garcia et al. , 2016). For each root tip (n>10), the number of mitotic events was counted directly under the microscope.
Accession Numbers Sequence data from this article can be found in the Arabidopsis Genome Initiative or GenBank/EMBL databases under the following accession numbers: RADA, At5g50340; RECG1, At2g01440; RECA2, At2g19490; RECA3, At3g10140; ANAC044, At3g01600; ANAC085, At5g14490; KNOLLE, At1g08560; CDKB1;2, At2g38620; EHD2, At4g05520; PLE, At5g51600; MYB3R3, At3g09370; MYB3R4, At5g11510; CYCD3;1, At4g34160; CYCD3;2, At5g67260; CYCD3;3, At3g50070; MCM2, At1g44900; MCM3, At5g46280; PCNA1, At1g07370; PCNA2, At2g29270; CDT1a, At2g31270; CycB1;1, At4g37490; WEE1, At1g02970; BRCA1, At4g21070 ; RAD51, At5g20850 ; XRI1, At5g48720; SIM, At5g04470; SMR1, At3g10525; SMR2, At1g08180 ; SMR3, At5g02420; SMR4, At5g02220; SMR5, At1g07500; SMR6, At5g40460; SMR7, At3g27630; SMR8, At1g10690; SMR9, At1g51355; SMR10, At2g28870; SMR11, At2g28330; SMR12, At2g37610; SMR13, At5g59360; AOX1, NM_001249237; RBCS, At1g67090.
Acknowledgments We are grateful to  Dr. Sandra Noir  for help with flow cytometry, to  Dr. Esther Lechner  for vectors and technical advice and to  Dr. Patrice Polard  and  Dr. Bénédicte Michel  for helpful discussions. This work has been published under the framework of the  LABEX  [ ANR-11-LABX-0057_MITOCROSS ] and benefits from a funding from the state managed by the  French National Research Agency  as part of the  "Investments for the future" program.