dataesr/scientific-paragraphs-categorization huggingface dataset:
4 software package. The mass spectrometer was used in the reflectron mode with a negative polarity for LDI-MSI and a positive polarity for MALDI-MSI. Spectra were acquired in the mass range of m/z 100-600 for all (x, y) coordinates corresponding to the imaged tissue. The laser raster size was set at 35 microns. The signal was initially optimised by manually adjusting the laser power and the number of laser shots fired. Accordingly, full-scan MS experiments R e v i s e d m a n u s c r i p t 12 were run by accumulating 400 laser shots per raster position and by using the laser power leading to the best signal-to-noise ratio. Image acquisition was performed using the Flex Imaging 4. 0 (Bruker Daltonics) software package. The correlation of the target plate with the optical image was obtained from three distinct teaching points following the procedure of the Flex Imaging software (Bruker Daltonics).
A rotation of the arenas was done four times a day to avoid a position effect in the climatic chamber. Experiments started at the beginning of the nocturnal phase and ended 48 hours after. To analyse snail distribution, the position of each snail in the arena was reported. To evaluate lichen consumption, radula marks on lichen thalli were observed under stereomicroscope (Zeiss, France). The area of radula impacts was measured (in µm²/snail) with Labscope software (version 2. 0, Zeiss, France).
Tukey's post hoc pairwise comparisons were realised. As no differences between sampling sites were observed on the feeding score (χ 2 = 0. 69, df = 1, P = 0. 408), the results of both sampling sites were combined. All statistical analyses were made using R software V. 3. 4. 3 (R Core Team, 2017). The R packages used were: car, emmeans, lme4, nnet, MASS, MuMin and RVAideMemoire. R e v i s e d m a n u s c r i p t 14 conducted at the P2M2 Platform, thanks to Dr Alain Bouchereau, and with the technical assistance of Catherine Jonard and Nathalie Marnet, which are warmly thanked. Authors are also indebted to Dr Maxime Dahirel for his advices in statistics and to Dr Maxime Hervé who wrote the R script that referred to feeding choice experiments (Link to his page: https://www. maximeherve. com/r-etstatistiques, and package 'RVAideMemoire').
Ethical Statement The French Polar Institute (IPEV) is the authority that supported this research based on the advice of its scientific council. The sites visited during this study did not require any access authorization. All research and data reported here were obtained in compliance with all current French laws. Collecting and transport of specimens of the species Notodiscus hookeri were authorized by the Prefect of Illeet-Vilaine, France, licence N°35-120 delivered in October 2015. Table 1:  Results of various parameters of validation studies for usnic acid quantification.
Acknowledgments Subantarctic field trip was funded by l' Institut Polaire Paul-Émile Victor, Plouzané, France (IPEV , programme  136 ). Dr Damien Ertz  is acknowledged for the identification on the field of the lichen Usnea taylorii and for his help with the snails' collection. Julien Tommasino  and  Grichka Biver  are thanked for their contribution in producing a part of this data set. Aude Boutet ,  Julien Tommasino  and  Benjamin Ferlay  are warmly thanked for their help during the fieldwork. Sugars and polyols quantifications were.
For studies in DNBS treated Il10 -/-mice, gene expression profiling was performed using the TaqMan OpenArray Mouse Inflammation Panel plate (Life Technologies) designed by the manufacturer, that consists of 632 gene targets selected for their involvement in inflammatory responses. The cDNA (10 µl) was mixed with the TaqMan OpenArray Real-Time PCR Master Mix and loaded onto the cards using the AccuFill ™ System. The cards were cycled in an OpenArray NT Cycler System (Applied Biosystems) at the integrative microgenomic platform (@BRIDGe, INRA, Jouy-en-Josas) following the manufacturer's protocol. The same sample was systematically loaded in each TaqMan OpenArray and used to check the reproducibility between the plates. Data were extracted using OpenArray Real-Time qPCR Analysis software (Applied Biosystems).
Principal component analysis, heatmap representation, and statistical analysis of the TaqMan OpenArray data. The R statistics environment was used for data analyses. Data obtained from TaqMan OpenArray experiments are represented either by Principal Component Analysis (PCA) plots or heatmaps. Rq values were used to build the PCA plots and heatmaps. Prior to PCA, we filtered the data using a one-way permutation test (oneway_test, R package "coin") to remove genes from the datasets for which the variation in expression was less informative (threshold set to p < 0. 01). PCA was then carried out on the filtered dataset using the R packages FactoExtra and FactoMineR. The number of genes included in the PCA analysis is specified in the figure legend for each comparison. Heatmaps were generated for genes showing a significant difference between the mono-associated mice and the GF group (p < 0.
The PCR amplicons were sent to the GeT-PlaGe platform (INRA, Toulouse) for sequencing using Illumina Miseq technology. Single multiplexing was performed and the multiplexes purified and loaded onto the Illumina MiSeq cartridge according to the manufacturer's instructions. Raw sequences were analyzed using the FROGS pipeline to obtain the OTU (operational taxonomic units or phylotypes) abundance table, phylogenetic tree, and taxonomic table using the default parameters  29. Statistical analyses of the 16S rRNA sequences were performed from the FROGS-generated outputs using R and environment version 3. 2. 3. Calculations of within-community diversity (α-diversity), between-community diversity (β-diversity), and relative abundance taxonomic summaries were performed using the add-on package "Phyloseq".
Statistical analyses. R 3. 3. 1 and GraphPad 5 software were used to produce graphs and for statistical analyses. Data are expressed as the mean ± standard deviation in scatter plots. Differentially expressed genes from OpenArray data were obtained with non-parametric multiple comparison tests using false discovery rate (FDR) corrected p-values (the threshold for significance of differential expression was set to p < 0. 05). Comparisons of other quantitative variables were performed using the non-parametric Mann-Whitney test (p < 0. 05 was considered significant).
2D ), whereas there was a significant increase in the percentage of proliferative epithelial cells in only the colon in the CEC WT group (Fig. 2D ). We then assessed the effect of E. coli strains on intestinal permeability in the ileum and colon. We monitored the para-cellular passage from the mucosal to serosal side of high-and low-molecular weight molecules, FD4 (Fig. 2E ) and FSA (Fig. 2F ), respectively, in an Ussing chamber. There were no differences in permeability between the groups. Among the panel of tight junction or cell adhesion proteins we tested [claudins-4,-5,-7,-8,-12,-15, -17, ZO-1 and F11r (data not shown), Cld2 and Cld3 (Supplementary Fig. 5C, D )], we only observed greater immunostaining of cadherin-1 (Cdh1) in the CEC WT than the GF WT mice (Fig. 2G, H ). These data show that intestinal barrier function and epithelial integrity are preserved in gnotobiotic WT mice.
6 ). We further investigated the effect of CEC and Nissle on the ileal and colonic gene expression profile in gnotobiotic IL10 -/-mice. We first randomly sampled four of the 10 individuals belonging to the GF IL10 and CEC IL10 groups to assess the ileal gene expression profile using the customized gene-expression array plates. The data obtained were then compared to those previously obtained for GF  WT  and CEC WT mice. PCA showed the CEC IL10 group to strongly diverge from the others along PC1 (Fig. 3A ). There was a striking difference of the gene expression profile from that of the CEC WT group, and the difference between the CEC IL10 and GF IL10 groups was higher than that between the CEC WT and GF WT groups. This initial screening suggests that the intestinal responses to E. coli of IL10 -/-mice are different from those of WT mice.
4E, F ). But in contrast to WT mice, this increase also occurred in the colon of IL10 -/-mice (Fig. 4E, F ). Intestinal permeability was assessed in vitro at the level of the ileum and the colon. No difference in FSA passage among the groups was observed (Fig. 4G ). In contrast, the ileal transepithelial conductance of CEC IL10 and Nissle IL10 mice was lower that than of the GF IL10 mice (Fig. 4H ), suggesting a tendency to a lower intestinal permeability. Taken as a whole, this data reveals that CEC and Nissle do not alter intestinal permeability in a model of predisposition to inflammation. These strains can even impact positively on some markers of epithelial barrier function.
Acknowledgements We thank the  @BRIDGe platform ,  UMR 1313  GABI, 78350, Jouy-en-Josas, France, for technical support and advice, in particular  C. Bevilacqua  and  M. N. Rossignol  for the high-throughput gene expression experiments and the histology facility team, including  J. Riviere ,  A. Boukadiri  and  M. Violette. We also thank the  IERP and ANAXEM Animal Facilities of the INRA of Jouy-en-Josas  for the animal experiments and technical support.
Background: The demographics and management of patients with multiple sclerosis (MS) differ across geographical regions, but it is unclear whether/how these differences affect treatment outcomes. The aim of this post-hoc analysis was to assess teriflunomide use and patient-reported outcomes in the United States (US) and the rest of the world (ROW) in the phase 4 Teri-PRO study (NCT01895335). Methods: In the phase 4, real-world, Teri-PRO study, patients with relapsing forms of MS received teriflunomide for 48 weeks according to local labeling. The primary endpoint was treatment satisfaction measured using the Treatment Satisfaction Questionnaire for Medication Version 1. 4 (TSQM 1. 4). Secondary endpoints included scores on the Expanded Disability Status Scale (EDSS), Multiple Sclerosis Performance Scale (MSPS), and Patient-Determined Disease Steps (PDDS), and occurrence of adverse events.
, 2018). In line with these differences, the perceptions of patients and neurologists regarding various aspects of their disease management differ across countries. In one survey, patients in Spain perceived their neurologist to be the sole decision maker when selecting a treatment, whereas patients in the US, UK, Italy, and Germany were less likely to hold this view  (Tintoré et al. , 2016). Teriflunomide is a once-daily oral immunomodulator approved for the treatment of RMS in over 80 countries, including the US and countries of the EU. Treatment satisfaction in patients receiving teriflunomide was assessed in the phase 4 Teri-PRO study (NCT01895335) using patient-reported outcome (PRO) measures  (Coyle et al. , 2017). Patients receiving teriflunomide reported high Treatment Satisfaction Quality of Medication (TSQM) scores both for global satisfaction and the effectiveness, side effects, and convenience subscales.
Acknowledgments The authors would like to thank the patients, their families, and all investigators who provided data for this report. Medical writing support under the direction of the authors was provided by  Francesca Murphy  ( Onyx, London, UK ), funded by  Sanofi , according to Good Publication Practice guidelines (link). The manuscript was reviewed for scientific accuracy by  Darren P. Baker, PhD ,  Jonathan Valenzano, PharmD , and  Karyn Liu, PhD  of  Sanofi. The sponsor was involved in the study design, and collection, analysis, and interpretation of data, as well as verification of the data presented in the manuscript. The authors had unrestricted access to study data, were responsible for all content and editorial decisions, and received no honoraria related to the development of this publication.
ACKNOWLEDGMENTS We would like to thank  Nathalie Leonhardt  ( CEA/Cadarache ) for help with the measurements of stomatal density/index. We are also grateful to the GRAP platform ( CEA/Cadarache ) for growing plants under normal and stress conditions. We also thank  Pierre Chagvardieff  ( CEA/Cadarache ) for support and  Giovanna Loro  for her assistance. The mbs1 mutant was received from  Ralf Bock  ( Max Planck Institute, Golm, Germany ). The scl14 and OE:SCL14 were a kind gift of  Christiane Gatz (Gottingen, Germany ). This work was funded by the  French National Research Agency  ( ANR  project  SLOSAM ,  14-CE02-0010-02 ) (M. H. ). Y. M. was supported by the  European Union  (project  WATBIO , grant agreement no. 311929 ) and the  French National Research Agency (ANR , project  ORCA , grant agreement no.
Policies, Plans, Initiatives, and Actors in the Livestock Sector and in Climate Change in Colombia We used the data from the bibliographic review of policies, plans, programs, and projects regarding climate change, to construct a timeline of the livestock sector in Colombia 1991-2017 (Figure  1 ). The timeline shows how the country has developed diverse initiatives and how it has started a series of policy instruments to achieve the coordination and structuring of climate change initiatives. In 2011, CONPES sought to consolidate institutional strategy to articulate policies and actions in climate change matters (CONPES #37000 of 2011). In 2016, the National System of Climate Change (SISCLIMA) was established by decree, as a coordinating and management platform for adaptation to and mitigation of climate change matters (Decree 1298 of February 24, 2016).
The qRT-PCR reaction consisted of gene-specific primers (Table  S2 ), PerfeCTa SYBR Green FastMix Low ROX (Quanta Biosciences, Beverly, MA, USA), and the cDNA template. Thermal cycling conditions were 95°C for 3 min followed by 95°C for 15 s, 60°C for 30 s, and 72°C for 30 s for 40 cycles. Elongation factor 1-alpha (Solyc06g005060) and ubiquitin (Solyc07g064130) were used as housekeeping genes  (Fragkostefanakis et al. , 2014 (Fragkostefanakis et al. , , 2016)). Data were analyzed using the 2 ÀDDCt method  (Livak & Schmittgen, 2001). Immunodetection analysis was performed using an antibody generated against a recombinant full-length HsfA2  (Scharf et al. , 1998; Mishra et al. , 2002). The green fluorescent protein (GFP)-HsfA2 isoforms in the minigene system were detected by a monoclonal GFP antibody (Roche) and a mouse horseradish peroxidase (HRP) conjugated secondary antibody (Thermo Fischer Scientific, Waltham, MA, USA).
Genome-wide association study Forty-two accessions for which resequencing data were available were measured for thermotolerance. We used GATK UNI-FIEDGENOTYPER v. 3. 8  (Depristo et al. , 2011)  to obtain a set of genome-wide variants in these accessions. From this set, we ended up with 1469 000 variants that were single nucleotide polymorphisms (SNPs), biallelic, genotyped in at least 41 of the 42 accessions, with a minimum allele frequency of 5% in our dataset. We then used EMMAX  (Kang et al. , 2010)  with an identity by state kinship matrix and default parameters to calculate associations between each variant and the thermotolerance phenotype. Associations with P < 10 À4 were considered to be significant. Linkage disequilibrium (LD) for all polymorphisms of HsfA2 was calculated using PLINK v.
Classification of resequenced tomato accessions in phylogenetic groups Whole-genome sequencing data are available for 601 accessions  (Zhu et al. , 2018). Short reads from all accessions were downloaded from NCBI-SRA and aligned to the S. lycopersicum reference genome (Tomato Genome Consortium, 2012) using BOWTIE2 v. 2. 50  (Langmead & Salzberg, 2012)  with default parameters. Reads mapping to multiple locations were removed using SAMTOOLS v. 1. 7 (parameter -q 5), duplicated reads were removed using Picard Tools' MARKDUPLICATES (http://broadinsti tute. github. io/picard) and indels were realigned using  GATK REALIGNERTARGETCREATOR and INDELREALIGNER v. 3. 8 (Depristo et al. , 2011). These 601 resequenced accessions where assigned to a phylogenetic group by comparison with the accessions classified in  Blanca et al.
(2015). In Blanca et al. 's work, 1008 tomato accessions were classified into phylogenetic groups using 8700 genome-wide SNPs genotyped with the SolCAP Infinium Chip  (Blanca et al. , 2015). We genotyped the 601 resequenced accessions at the SolCAP Infinium array positions (indicated in the ITAG2. 4_-solCAP. gff3 file available at www. ftp. solgenomics. net) using GATK UNIFIEDGENOTYPER with default parameters. This list of variants was filtered to leave only biallelic SNPs, resulting in a total of 7486 variants, which were merged with the published matrix containing the genotypes for 1008 accessions  (Blanca et al. , 2015). In all, 1630 variants that did not agree between the two datasets were removed, and the resulting list was filtered for loci in LD using the 'LD' pruning option of PLINK with parameters --mind 0.
1 --geno 0. 1 --indep 50 5 2. 8  (Chang et al. , 2015). A phylogenetic tree was estimated from the final matrix (1536 variants in 1609 accessions) using the APE package in R and the neighbor-joining method including S. pennellii LA0716 as a root  (Paradis et al. , 2004). The resulting tree was plotted using the GGTREE package in R  (Yu et al. , 2017). Tomato accessions in the tree were classified manually taking into account the previously described classification  (Blanca et al. , 2015)  and their position in the tree (Table  S3 ). All 601 accessions were genotyped for the three intronic variants of interest (SL2. 50ch08 52380445, 52380439 and 52380421) by calling SNPs simultaneously in all alignment files using GATK UNIFIEDGENOTYPER v. 3. 8.
5a ). Consequently, in our dataset we find three haplotypes for intron 2: HsfA2 AAA present only in WILD; HsfA2 GAG in PIM and SLC; and HsfA2 GGG in PIM, SLC or SLL (Fig. 5a ). The splicing profile of HsfA2 intron 2 was examined in 33 tomato genotypes carrying different haplotypes at this intron. All distant wild tomatoes having the HsfA2 AAA haplotype lack HsfA2-Ic and show significantly enhanced splicing of intron 2, with HsfA2-II transcripts comprising c. 90% of the total HsfA2 transcripts (Fig. 5b, c ). Compared with this, retention of intron 2 in accessions with a HsfA2 GGG haplotype was observed for 50% of the transcripts (Fig. 5c ). Instead PIM and SLC accessions with the HsfA2 GAG allele show an intermediate and variable splicing profile (Fig. 5c ). We observed a correlation between splicing efficiency and thermotolerance (r = 0.
Acknowledgements We acknowledge  Lutz Nover ,  Elizabeth Vierling ,  Christos Bazakos  and  Miltos Tsiantis  for critical reading and suggestions. This work was supported by grants from  DFG Germany  to SF (413737959) and to ES ( SFB902 ), a  SPOT-ITN Marie Curie grant  ( 289220 ) to ES,  K-DS  and AB, and a  China Scholarship Council (CSC)  to YH.
Thus, to test this hypothesis, we analyzed by RT-qPCR the RNA steady state level of the centromeric 180 bp repeats and of the flanking pericentromeric heterochromatic domains containing 5S rRNA before (time point 0) and after UV-C irradiation (2h and 24h). We found that in WT plants the 180 bp and the 5S transcripts levels increased 2h upon UV-C exposure and come back to initial level at 24h (S11A and S11B Fig). In ddb2, dcl4 and ago1 plants we also measured an increase level of 180 bp and the 5S transcripts levels upon UV-C irradiation whilst in uvr3 phrI plants they decreased (S11A and S11B Fig). This shows that UV-C exposure released expression of particular centromeric and pericentromeric sequences and that this response relied on the DR pathway. Collectively, our data highlighted that UV-C exposure induced the release of silencing of particular repeats as well as structural changes of chromocenters and 5-mC distribution.
DMRs calling Upon mapping, the methylation levels were calculated with methratio. py. Differentially Methylated Regions (DMRs) between untreated and treated plants of the same genotype were determined according  Daccord et al. (2017)   [70]  considering 200 bp sliding-windows with an overlap of 50 bp (sliding-window-pipeline). DMRs were identified using the difference between identical windows and upon filtering. Consecutive windows exhibiting the same methylation change (gain or loss) were joined and methylation level recalculated. DMRs were called for a DNA methylation difference (p< 0. 05 according Wilcoxon signed-rank test), within the same genotype, higher or equal than 0. 4 for CG, 0. 2 for CHG and 0. 1 for CHH methylation contexts. We re-analyzed with our method previously published BS-seq datasets  [38]  for met1 (GSM981031), cmt2 (GSM981002), cmt3 (GSM981003), drm1/2 (GSM981015), nrpd1 (GSM981039), ago4 (GSM980991) and ago6 (GSM980993).
43 μm slice distance. All pictures had a final voxel size of 0. 1014 x 0. 1014 x 0. 4300 μm^3. The image quantification was performed on ImageJ1. 52o using a homemade plugin called Nucl. Eye (https://github. com/mutterer/Nucl. Eye). This plugin allows either an automatic or a manual delimitation of all nuclei on the z-max compiled image in order to quantify size and signal intensity of each nuclei and all internal spot like entities. Using the information of individual spot (intensity, surface) and nuclei surface, the Chromocenter Occupancy (CO) was defined as percentage of surface occupied by all bright DAPI spots (chromocenters) in the corresponding nucleus. Intensities and surfaces of each chromocenter and those of the whole nucleus were used to calculate their relative intensities and surface.
To make up slides, the stigmas were excised and placed on a cube of gelatine-fuchsin, a coverslip was placed on top of the gelatine cube and gentle heat was applied to melt the gelatine  58. Stigmatic pollen loads were then estimated by counting either avocado, mango or macadamia pollen grains under 200x magnification. We also collected a second virgin control stigma (bagged and unvisited) allowing us to assess other potential sources of pollen to stigmatic totals  5. Across the three crops, SVD data was collected over 4 years between 2014 and 2017. For pollen data analysis, we opted to use the most conservative estimate available with our first choice being the median of pollen deposition estimates  59. Due to the distribution of the pollen deposition values, the median value in our data sets was most often zero, hence we opted to use mean deposition values.
We accounted for non-insect related pollen deposition on each stigma, with the mean pollen value from the collected control stigmas for each data set subtracted from individual SVD values for each insect taxa  60  (SI Table  6 ). We calculated 'pollinator effectiveness' by multiplying visitation rate and mean SVD for each field defined visitor group to gain an understanding of their pollination effectiveness in a given crop  9, 60, 61. Pollen deposition information was not collected for rare or less abundant visitor species observed in our visitation networks. However, rather than disregarding their contribution we grouped these visitors together and multiplied their visitation rate by the lowest mean deposition value from an insect taxon collected to represent the most conservative estimate of their effectiveness possible.
Landscape composition. Landscape composition was defined as the proportion of different land uses around each site and was quantified with ArcMap 10. 2 based on state and national land use mapping data sets  [62] [63] [64]  using the Australian Land Use and Management (ALUM) 3-tier land use classification system (SI Fig. 9 ). To standardise our use of land type definitions in this study we selected second tier ALUM classifications that could potentially provide resources (floral and nesting) for pollinator taxa surrounding our study orchard sites. Land use types were quantified for three perimeters (500 m, 1 km and 2 km) surrounding orchard sites where overlap in perimeters did not occur (i. e. several mango sites in Bundaberg and avocado sites in Sunraysia were excluded from these analyses due to their close proximity) in all three regions and years corresponding to observation surveys.