dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments The authors wish to thank the numerous people involved in this study over twelve years (2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014)(2015)(2016)(2017)(2018)(2019), especially:  E. Lucas ,  E. Poulbassia ,  P. Rousse ,  L. Vanhuffel ,  D. Vincenot  ( Chambre d'agriculture de La Réunion );  Y. Soupapoullé  (Arifel);  C. François  ( Coopérative Vivea );  B. Longoras  ( Groupement de l'Agriculture Biologique );  M. Marquier  (FDGDON);  T. Nurbel  (Armefhlor);  D. Boyer  ( Mairie de Salazie );  L. Maillary ,  B. Debenay  (DAAF);  C. Ajaguin Soleyen ,  A. Allègre ,  H. Brouchoud ,  E. Douraguia ,  T. François ,  B. Gilles ,  M. -L. Moutoussamy ,  P. -G. Vogt  (CIRAD). Acknowledgments are also extended to all chayote growers who contributed to this project, especially  C. Boyer ,  S.
Mice, Borrelia afzelii, and Ixodes ricinus ticks We used Mus musculus BALB/c mice as the rodent host because we have a history of successful experimental infections with this mouse strain  [45] [46] [47]. During the study, the mice were maintained in individual cages and were given food and water ad libitum. The mice were experimentally infected via tick bite with B. afzelii strain NE4049. This strain was originally isolated from an I. ricinus tick in Switzerland and has multilocus sequence type (MLST) 679 and strain identi cation number 1887 in the Borrelia MLST database, and ospC major group A10. We chose to work with strain NE4049 because it is highly infectious to both rodents and I. ricinus ticks  45, 46, 48. The adult female I. ricinus ticks used to produce the eggs and larvae for this study were collected from wild roe deer captured in the Sylve d'Argenson forest near Chizé, France.
Statistical Methods Statistical analyses were performed using RStudio Version 1. 2. 5042. The lm() and glm() functions in the base package were used to create the Linear Models (LMs) and the Generalized Linear Models (GLMs), respectively. The lmer() and glmer() functions in the lme4 package were used to create the Linear Mixed effects Models (LMMs), and the Generalized Linear Mixed effects Models (GLMMs), respectively. The corrplot() function in the corrplot package was used to graph the correlation matrix of the life history traits of the immature I. ricinus ticks. Effects with p-values < 0. 050 were considered statistically signi cant. After Bonferroni correction for 5 life history traits, p-values < 0. 010 were considered statistically signi cant.
Prevalence of B. afzelii infection in unfed I. ricinus nymphs A total of 289 unfed nymphs were tested for B. afzelii via qPCR. Of the 289 nymphs, 106 nymphs had fed as larvae on uninfected control mice and 183 nymphs had fed as larvae on infected mice. The prevalence of B. afzelii infection in the nymphs that fed as larvae on the infected mice (71. 0% = 130/183) was signi cantly higher (25. 1x) compared to the nymphs that fed as larvae on the uninfected control mice (2. 8% = 3/106; proportion test: c 2 = 122. 97, df = 1, p < 0. 000001). The 3 nymphs that fed as larvae on uninfected mice, but that tested positive for B. afzelii on the qPCR are false positives (these 3 nymphs had high Cq values of 39. 62, 39. 74, 40. 22; see section 3 of the ESM). Data on the variation in host-to-tick transmission of B.
The aim of the Biorisk-MSN mission was to expose dry incubated eggs to low orbit radiation. Unfortunately, no data is available concerning the resistance of the fish eggs as the equipment had no temperature sensor and the plastic dishes reached 95 °C, deforming the plates, and the eggs died due to the high temperature and vacuum contact  (Baranov et al. , 2009). To study the fish response at early stage to microgravity, two missions using medaka fish were performed on ISS, in 2012 and 2014. Each time a Soyuz rocket sent 24 juveniles medaka (6 weeks after hatching, 16 mm) with the objective of rearing this population in the Aquatic Habitat (AQH) on the Kibo section of the ISS. Medaka fish in space and control fish from the same family on Earth were filmed. The movies showed that the fish became adapted to life under microgravity although despite an unusual swimming behavior.
This aspect will have a direct impact on the total energy required for an acceptable growth yield in the SAS. Although fish have a low oxygen uptake compared to other vertebrates (Figure  2 ), a regular supply is required. Oxygen dissolution in the water from hydroxyl extraction and oxygen from the regolith and/or from photosynthesis in plants cultivated in the BLSS must be synchronized with the biological demands of the fish. This requires the capacity to regularly collect, store and dissolve oxygen in the water column. The oxygen data from the CEBAS experiment on the STS-89 and STS-90 missions was analyzed to model this concept. Results based on the experimental MINI-MODULE (8. 6 L) showed different periods of oxygen accumulation and depletion in the aquatic habitat in plants (oxygen producer) and snails (oxygen consumer).
Studying the Feasibility of Sending Aquaculture Fish Embryos to the Moon: The Lunar Hatch Program In research underway since 2019, the Lunar Hatch program is investigating the feasibility of shipping embryonated aquaculture fish eggs to space for programmed hatching in a lunar BLSS. The hatched larvae would then be fed with local resources and reared until they reached an appropriate size for human consumption. The aim of the study is proof of concept based on experimental data collected first in ground-based trials, followed by test missions in low orbit, and concluding with a real flight to space, perhaps leading to the hatching of the first vertebrate on the Moon. The program focuses on the viability of European seabass (Dicentrarchus labrax) for such a project, by analyzing the potential effects on embryos of a Moon journey and the associated environmental changes.
Genome-wide CG hypomethylation is observed in the suppressor lines To test whether the suppression of the triploid block in 5-Azacytidine-treated jas-3 plants correlated with a transgenerational loss of DNA methylation, we performed wholegenome bisulfite sequencing (WGBS) (Supplemental Data Set S1). We performed comparative methylome analyses in the eM2 generation of the strong suppressor lines Aza1 (3. 7% collapsed seeds), Aza14 (11. 3%), Aza18 (6. 6%), and Aza25 (6. 3%) and the nonsuppressor lines Aza5 (27. 8%), Aza10 (30,7%), Aza16 (26. 9%), and Aza26 (28. 7%), which showed levels of seed collapse closer to the controls jas-3 (mean 33. 7%) and DMSO (mean 33. 4%). Indeed, in the suppressor lines, the strong loss of CG methylation was observed at protein-coding genes and transposable elements compared to the untreated jas-3 and DMSO controls (Figure  2A ; Supplemental Figure  S5 ).
Average CG methylation mapping to these DMRs is presented as a heatmap for untreated jas-3 (two replicates) and the DMSO controls (two replicates), suppressors, and nonsuppressors. C, Hypomethylated CG DMRs detected in each suppressor line were mapped to the genomic features annotated in the TAIR10 reference genome, showing that the majority of DMRs overlap with protein-coding genes and transposable elements (TEs). D, Venn diagram shows a significant overlap between differentially methylated 100-bp bins detected in the three strongest suppressor lines (Aza1, Aza18, and Aza25). The statistical significance of the observed overlap was calculated using the R package SuperExactTest  (Wang et al. , 2015). (Figure  3, B  and C ), thus indicating that certain epigenetic states were already fixed.
C, CG methylation of untreated jas-3, DMSO, eM2, and eM3 lines was mapped to 100-kb bins across the Arabidopsis genome. CG methylation levels in the DMSO, eM2, and eM3 datasets were then divided by the levels in jas-3 and plotted separately for all five chromosomes to show patterns of hypomethylation. This shows that for most of the genome, the distribution of CG hypomethylation is identical between the two eM3 lines, although there are particular loci where CG methylation is segregating. A schematic of each chromosome is illustrated below the metaplots, showing approximate centromere locations as black dots. 2015;  Martinez et al. , 2018; Batista et al. , 2019; Satyaki and Gehring, 2019). Therefore, we performed transcriptome analysis by mRNA sequencing of developing siliques collected 6-9 days post anthesis, as previously described  (Mizzotti et al.
, 2018). Comparisons between WT Col-0 and jas-3 mutant siliques revealed 668 downregulated and 1,804 upregulated genes in jas-3 (Figure  4A ; Supplemental Data Set S3). Similar analysis between WT and DMSO control plants showed a strong overlap between upregulated genes in untreated jas-3 and DMSO control plants (Supplemental Figure  S8  and Supplemental Data Set S3). These observations, together with the strong correlation between jas-3 and DMSO replicates (Supplemental Figure  S9 ), show that DMSO treatment does not induce major changes in the transcriptome of developing jas-3 siliques. We then compared suppressor Aza1 plants from the eM2 generation with the DMSO controls, finding that 470 genes were downregulated in Aza1 eM2, while only 48 were upregulated (fold change 52, P 5 0. 01) (Supplemental Data Set S3).
DMRs in the CG and CHG contexts were defined as 100-bp bins containing at least four or five differentially methylated CGs or CHGs and with an absolute methylation difference of at least 0. 4 or 0. 35, respectively. Regions with ectopic CHG methylation were defined as 100-bp bins without methylated CHG in the control dataset (untreated jas-3), and containing at least three differentially methylated CHGs with an absolute methylation increase of at least 0. 15 in the suppressor lines. Around 100-bp bins localizing within 200 bp of each other were merged, and bins that merged at least once were considered to be DMRs.
RNA sequencing and analysis Total RNA was extracted from three siliques 6-9 days after anthesis, as previously described  (Mizzotti et al. , 2018)  using an RNeasy Plant Mini Kit (Qiagen) following the manufacturer's recommendations for seed tissues (RLC buffer). Sequencing of messenger RNA was performed by BGI Genomics (Hong Kong) using DNBSEQ technology. Highquality raw reads were aligned to the TAIR10 genome using STAR  (Dobin et al. , 2013). Reads were counted and normalized using the R package DESeq2  (Love et al. , 2014). We considered differentially expressed genes to be those displaying a log2 fold-change 52, and with an adjusted P 5 0. 01. Graphical outputs were produced using the R packages ggplot2, pheatmap, and ComplexHeatmap. The list of PEGs used in the comparative analysis is presented in Supplemental Data Set S4.
Statistical analysis Statistically significant differences in the percentage of collapsed and nongerminated seeds (Figures  1, A  and C  and 3A; Supplemental Figure  S4A ) were calculated by one-way analysis of variance (ANOVA) with a post hoc Dunnett test, using the R packages "ggpubr" and "multcomp". A Wilcoxon test was used to compare the mean values between the amount of diploid pollen (Supplemental Figure  S1B ), using the R package "ggpubr". The statistical significance of the observed overlaps between differentially methylated 100-bp bins (Supplemental Figure  S2D ) and between differentially expressed genes (Supplemental Figure  S8 ) was calculated using the R package "SuperExactTest"  (Wang et al. , 2015). These analyses are presented in Supplemental File S1.
Funding This work was supported by the grant " EpiHYBRIDS " from the  French National Agency of Research  ( ANR-19-CE12-0008 ) and by an installation grant provided by the  Plant Biology and Breeding (BAP) department of the French National Research Institute for Agriculture, Food and Environment (INRAE)  to F. B. This work was also partially supported by the  EUR SPS-GSR  ( ANR-17-EUR-0007 ). The work of K. D. and C. K. was supported by a grant from the  Knut and Alice Wallenberg Foundation  to C. K. (grant # 2018-0206 ).
Strawberries supply chain Strawberries were considered grown open-field in Spain, and sold in the South of France, to mimic the case where strawberries are grown far away from the wholesaler location which is a sub-optimal, long circuit of distribution for the environmental assessment. A typical supply chain for strawberries was constructed based on interviews done with French wholesalers and based on literature reviews as described elsewhere  (Matar et al. , 2020)  (Fig. 1 ). Mean temperatures and mean storage durations were chosen to represent a standard storage scenario in the pre-supermarket stages. Percentages of losses for the pre-supermarket stage come from questionnaires  (Matar et al. , 2020)  and has been validated by comparison with literature data on the topics  (Gitz et al. , 2014; Gustavsson and Stage, 2011a).
Cold chain and electricity consumption. The energy consumption was estimated using a tool provided by Intelligence Energy Europe (ICE-E)  (Evans, 2013). This simulation tool was developed to identify the energy-saving potential of cold store equipment and technologies on the basis of datasets from 294 cold stores, mostly from EU countries. Each dataset included the temperature of the store, the area and volume of the store, food throughput and energy usage per year. 2. 2. 1. 4. 1. Precooling, wholesalers, central purchase and supermarket (reception and storage substeps). The refrigerated chambers at the precooling, wholesalers, central purchase and supermarket (reception and storage room) are considered the same and the infrastructure of the ecoinvent dataset "Cold room based on: Operation, reefer, cooling {GLO}| 40-foot, high-cube, R134a as refrigerant" is used  (Ecoinvent, 2016).
Impact assessment method Environmental impacts were assessed with the Environmental Footprint method version 2. 0 implemented in Simapro software (v9. 0. 0. 48). This method has been selected as recommended by the European union for product environmental footprint  (Fazio et al. , 2018). The impact categories considered were: acidification terrestrial and freshwater, cancer human health effects, climate change, ecotoxicity freshwater, eutrophication marine and freshwater, eutrophication terrestrial, ionizing radiation (human health), land use, non-cancer human health effects, ozone depletion, photochemical ozone formation, resource useenergy carrier, resources usemineral and metals, respiratory inorganics and water scarcity.
Uncertainty analysis A Monte-Carlo approach was used to assess uncertainties on data and food losses parameter from farm to fork. Environmental impacts of the scenarios were calculated 1000 times. For each run, a random value of each parameter, within a define range, is considered. Considered stages of the farm to fork system and values for the food losses are reported in Table  1. Distributions are considered uniform for this parameter. Pairwise comparisons were performed. It allows us to determine for each comparison the percentage of occurrence for which one scenario best perform compared to the other. First uncertainty analysis was performed considering EMAP benefit at consumer's level only. A similar efficiency was assumed for all EMAP technologies and benchmark at the supermarket level, i.
For each impact category, the most impacting scenario is normalized at 100 %. The other scenarios are expressed relatively to the most impacting one. Raw data could be downloaded at https://doi. org/10. 5281/zenodo. 3938995. counterbalance the indirect environmental benefit made by reducing food losses (Figure  A3, d )). Standard, commercial EMAP (EMAP STD ) used alone (without combination with cold chain) could not reduce significantly the environmental impacts of the supply chain compared to the exclusive use of the cold chain in the conditions investigated here. Considering now the optimal EMAP solution (EMAP OPT,25 • C,3 d ), environmental impacts of EMAP OPT,25 • C,3 d and MPP 5 • C,3 d were in the same range, for all impact categories (Fig. 5 ), except for ionizing radiation which was high for MPP 5 • C,3 d concomitantly to the use of nuclear power for cold chain.
Finally, for EMAP STD,25 • C,3 d versus MPP 5 • C,3 d , whatever the value of food loss parameter at supermarket (range from 10. 5 to 5 %), MPP 5 For each impact category, the most impacting scenario is normalized at 100 %. The other scenarios are expressed relatively to the most impacting one. Raw data could be downloaded at https://doi. org/10. 5281/zenodo. 3938995. • C,3 d was the best option from environmental perspective (result not shown). Indeed, it was impossible to compensate losses at households in EMAP STD,25 • C,3 d by losses decrease at supermarket. If EMAP is not fully optimized and fit to the strawberry needs in order to decrease product's losses at a maximum at both, supermarket and consumer levels, there is no environmental benefit in comparison with the use of cold chain at households.
2 % 6. 5 % 8 % Fig. 3. Contribution analysis of 1 kg of straw- berry at the gate of the supermarket. Consumer step is excluded of this analysis. Contributions of strawberry production, transport all along the postharvest chain, packaging used to pack strawberries, electricity used in the postharvest chain are highlighted (electricity used for strawberry production is included in "Produc- tion"). Other contributors (mainly other inputs needed for waste treatment processes) are gathered in the last "Others" contributor. Raw data could be downloaded at: https://doi. org/ 10. 5281/zenodo. 3938995.
Due to low number of reads one sample of the C alt group (2236 reads) and one of the NegSF group (3040 reads) were excluded from further analyses. Sequences were clustered (d = 1 + d = 3) using Swarm and chimeras were removed. The remaining clusters were filtered. Clusters that were present in at least 7 samples and with abundances greater than 0. 005% of total sequences  [29]  were kept as OTUs (operational taxonomic units). Taxonomic affiliation of OTUs was obtained using the Silva132 database with a minimum pintail quality of 80  [30]. Samples had on average 28,015 ± 8698 reads (min: 5586, max: 46184) with 266 OTUs represented (98 ± 28 OTUs per sample).
Statistical analyses Statistical analyses were performed using R software version 4. 0. 2. The microbial composition was analysed with the phyloseq package  [31]. For alpha and beta diversity analyses, samples were rarified to even depth (5586 reads). Beta-diversity was determined using the Bray-Curtis dissimilarity method and plotted by non-Metric Dimensional Scaling (nMDS) ordination method. To assess group differences an ADONIS pairwise test with the Bray-Curtis distance was carried out. A Partial Least Squares Discriminant Analyzis (PLS-DA) was performed to determine the most discriminant OTUs separating NegSF and PosSF geese using the R mixOmics package  [32]. Taxa differential abundance analyses and PLS-DA were performed on unrarefied data with OTUs with abundances above 0. 1% of total sequences in at least one experimental group, which was considered as a quantitative threshold.
4c , Supplemental Table  2 ). When performing taxonomic affiliations on OTUs with abundances above 0. 1% in at least one experimental group 6 phyla, 31 families and 52 genera were observed in the overall dataset. Results are presented at phylum (Fig. 5a-b ; Supplemental Table  3 ), family (Fig. 5c-d ; Supplemental Table  4 ) and genus levels (Fig. 5e-f ; Supplemental Table  5 ). Firmicutes and Proteobacteria were the most abundant phyla with Lactobacillaceae and Peptostreptococcaceae of the first mentioned phylum being the most abundant families. In the conventional system, the proportions of Epsilonbacteraeota (-12. 3 pts. , P < 0. 05) and its sole genus Helicobacter from the dominant family Helicobacteraceae were lower after steatosis induction (OF) compared to C conv birds while the proportion of Proteobacteria was not significantly modulated but the proportions of two of its dominant families, Burkholderiaceae and Sphingomonadaceae, were significantly increased (+ 20.
Acknowledgements We thank  Hélène Manse  for performing the biochemical analyses and the  Get-PlaGe INRAE  team for the MiSeq sequencing of our samples. We are grateful to the  Genotoul bioinformatics platform Toulouse Occitanie (bioinfo Genotoul , doi: https://doi. org/10. 15454/1. 5572369328961167E12 )for providing computing and storage resources. The advice and technical assistance of the staff of the goose and ducks Breeding Station (Coulaures, France), especially  C. Mondoux , are acknowledged.
The maximum quantum yield of photosystem II (Fv/Fm) was measured on the same days using a JuniorPAM fluorometer (Walz, Germany). The sporophytes were dark-acclimated for 20 min prior to the measurement. After the last measurement, the kelp sporophytes were frozen in liquid nitrogen and kept at -80 • C for the molecular detection of the endophyte in the kelp tissue. The growth curves and Fv/Fm graphs were drawn with GraphPad prism (GraphPad Prism Software, Inc. , United States) and SPSS was used for statistical analyses (IBM Corp. Released 2015. IBM SPSS Statistics for Windows, Version 23. 0. Armonk, NY, United States: IBM Corp. ). Normality of the data and homogeneity of variances were tested with the Shapiro-Wilk test and the Levene test, respectively. Subsequently, data were analyzed with one-way ANOVAs.
Endophyte Detection Direct microscopic observation was not adapted to the observation of endophyte spore settlements after 2 weeks, as first tested on two L. digitata plantlets, co-cultivated with endophytes. We therefore used a qPCR-based molecular approach: DNA extraction and qPCR quantification of endophytes in the hosts were performed as described previously  (Bernard M. et al. , 2018). In total, up to 15 individuals of S. latissima and 13 individuals of L. digitata from three independent co-cultivation bioassays with L. elsbetiae as well as 3 randomly chosen control sporophytes of each species were analyzed by qPCR for the detection of L. elsbetiae DNA using specific ITS primers. Cycle threshold (CT) values were calculated with the LightCycler 480 Software (Roche, Germany): endophyte DNA was amplified with a maximum of 33 cycles, and above 34 cycles, it was considered as undetectable.
, 2011)  with the default options. The quality of the assembly was assessed by re-mapping the cleaned reads using the bowtie2 aligner  (Langmead and Salzberg, 2012). Transcript abundance was estimated in TPM with PERL scripts implemented in Trinity. The quality of the transcriptome assemblies was evaluated by using BUSCO v2. 0  (Simão et al. , 2015)  with eukaryote dataset and redundancy further reduced according to the TPM value. Gene annotation was performed with a Blastx search against the NCBI-NR (Release 239) and the Uniprot databases (Release 2020_02) with an E-value cut-off of 10 -5. Furthermore, genes were assigned to 2nd level GO subcategories within the three root categories molecular function, cellular component and biological process using  Blast2GO (Conesa et al. , 2005). Differential gene expression between the control and the cocultivation treatments was determined separately for the 24 and 48 h samples using DESeq2  (Love et al.
, 2014). Log2 fold change values ≥ 0. 7 and ≤ -0. 7 with a p-value < 0. 01 were considered to be up-and downregulated, respectively. Heat maps were plotted using the R package pheatmap. The genes that were differentially expressed in both species were compared with Blastn (E-value cut-off of 10 -5 ) against each other in order to identify common DEGs.