dataesr/scientific-paragraphs-categorization huggingface dataset:
Methodologies for dietary exposure assessment in animals Exposure to fumonisin by livestock is a function of its concentration in their diets and the amount of the diet consumed. In the absence of a comprehensive database on the amounts or types of feed consumed by livestock in the EU, estimates of feed consumed for each of the main categories of farmed livestock and companion animals are based on published guidelines on nutrition (e. g. Carabano and Piquer, 1998; NRC, 2007a,b; Leeson and Summers, 2008; McDonald et al. , 2011; EFSA FEEDAP Panel, 2012; OECD, 2013) , together with expert knowledge of production systems in Europe. For many farmed livestock and companion animals, their nutritional requirements are provided in commercially manufactured complete (compound) feeds. Where sufficient (reliable) data on the concentrations of fumonisins in compound feeds have been provided, these have been used to estimate exposure.
Methodology applied for risk assessment The CONTAM Panel applied the general principles of the risk assessment process for chemicals in food as described by WHO/IPCS (2009), which include hazard identification and characterisation, exposure assessment and risk characterisation. The principles described by WHO/IPCS (2009) and EFSA guidances pertaining to risk assessment have been applied for the present assessment. For details on the specific EFSA guidances applied, see Appendix A. The absorption, distribution, metabolism and excretion, (ADME) of fumonisins was reviewed by EFSA in 2005 (EFSA, 2005) and, more recently in 2018  (EFSA CONTAM Panel, 2018) , in an opinion addressing the appropriateness to set an HBGV for fumonisins and their modified forms in humans. Based on a limited data set in laboratory species, farm animals and humans, it was concluded that, upon oral exposure, fumonisins display a limited bioavailability (3-6%) and exhibit peak plasma levels a few hours after the exposure.
The study suggests that, upon oral exposure of cattle, FB 1 is largely excreted via the faecal route and to a lesser extent via urine; faeces also contain a measurable amounts of hydrolysed metabolites. Prelusky and collaborators (1995)  investigated FB 1 kinetics in four dairy cows (452-630 kg bw, unspecified breed) following either i. v. dosing (50 or 200 lg/kg bw) or oral gavage (1 or 5 mg/kg bw). Both FB 1 (LOD = 4 ng/mL) and HFB 1 (aminopentol) (LOD = 8 ng/mL) were assayed in plasma using an HPLC technique with fluorescence detection. Data from the i. v. administration best fitted a twocompartment model, with similar values irrespective of the dose. There was a very rapid distribution phase (t ½ a ~2 min) and a slower but still rapid elimination phase (t ½ b 15-18 min) with the parent compound and the metabolite being no longer detectable 120 min after dosing.
Turkeys Very little is known about fumonisin TK in turkeys. In the only paper that could be identified,  Tardieu et al. (2008)  investigated the comparative (i. v. vs oral) FB 1 TK in 1-week-old BUT9 male turkeys. For i. v. studies, eight individuals were dosed with 10 mg FB 1 /kg bw and blood samples were taken at different intervals up to 2,000 min after treatment. For studies using the oral route, further eight animals received a single dose of 100 mg FB 1 /kg bw and blood sampling was performed at 30-60 min intervals up to 600 min after dosing. Plasma and tissue levels of FB 1 were measured by an HPLC method (fluorescence detector, LOD 13 lg/kg). Data after i. v. dosing were best fitted to a threecompartment open model and were consistent with a rapid (t 1/2 a 3. 5 min) and notable distribution within the body (V d area around 1 L/kg) along with a rapid clearance (t 1/2 b 85 min, MRT 52 min, clearance around 8 mL/min per h).
Fish The available database from feeding studies giving fumonisins to fish is limited as only two feeding experiments with carp and one with each of channel catfish, African catfish and Nile tilapia have been identified. Fumonisins reduced the body weight gain of all species. EFSA (  2005 ) concluded that the available data at that time indicated a LOAEL of 10 mg FB/kg feed for carp, based on a study where 1-year-old carps (mean weight 127 g) were given feed containing 10 or 100 mg FB 1 /kg feed for 42 days  (Petrinec et al. , 2004). The diet was prepared by mixing Fusarium culture material into the feed. Pathological alterations in liver, endocrine and exocrine pancreas, kidney, heart and brain were reported from fish receiving the low dose feed. In another feeding study, 1-year old carp (120-140 g) were given FB 1 purified from Fusarium culture material mixed into the feed and given feed corresponding to 0.
As discussed above, estimates of exposure were previously published by EFSA (EFSA CONTAM Panel, 2014). A comparison of these with those estimated in this Opinion is given in Table  16. The CONTAM Panel noted the differences between the two assessments. In general, exposure estimates by EFSA CONTAM Panel (2014) were higher than for this Opinion (based on mean LB and UB levels for all species, at both the mean and P95 levels). There were no consistent differences between the two studies, although marked differences for individual species were observed at both LB and UB levels. However, a comparison of the database used in these two studies reveals large differences; in particular, the 2014 assessment was based on fewer feed samples, while in that database the differences between the LB and UB values were larger, particularly for the 95th percentile data.
Risk characterisation There is limited knowledge on the effects of Fumonisins and their modified and hidden forms on farm and companion animals. Furthermore, there is no comprehensive database on feed consumption by livestock in the EU. It has therefore not been possible to fully assess the risks of FBs and its modified and hidden forms for farm and companion animal health. Risk characterisation of the modified forms of FBs was not performed as no data concerning their occurence and toxicity was available. However, for a number of farm livestock and companion animal categories the chronic exposure of fumonisins (expressed as the sum of FB 1 , FB 2 and FB 3 ) in feed could be estimated at the mean and 95th percentile concentrations in animal diets based on expected feed intakes and example diets.
This information was available for a small proportion of the analytical samples. Thus, the levels were estimated by using the mean concentration of the closest feed group available and therefore adding additional uncertainty. Fumonisin occurrence is strongly related to climatic conditions, geographical area, and maize genotype. All these factors may affect not only the overall occurrence, but also the ratio between parent and hidden forms. Due to the lack of appropriate models, this should be considered as a factor of uncertainty. The Panel noted that the occurrence data in the EFSA database, used in the exposure assessment, were mainly from Northern Europe, where occurrence is generally lower than southern Europe. This could lead to a potential underestimation of exposure.
À Use of alkaline hydrolysis for hidden fumonisins determination + Extrapolation of the occurrence data mainly from Northern Europe to the whole of Europe À No occurrence data for modified forms in EFSA database À The number of samples were not equally distributed across all feed groups +/À Large proportion of left censored data in the final data set +/À Using the substitution method at the lower bound (LB) À Using the substitution method at the upper bound (UB) + Imputation of missing results for the calculation of the sum of fumonisins +/À Application of 1. 6 factor derived from maize to all feed components + Applicability of the 1. 6 to account for hidden forms to different animal species with different metabolism.
To assess potential recombination among the CFD alphasatellites we used RDP4  26  and detected one recombination event strongly supported by seven detection methods implemented in RDP4: the region from position 951 to 1099 in CFDA7 was identified as a possible recombinant with CFDA6. For details see Fig. S2. In addition to the CP-encoding DNAs S. 1 and S. 2 and the CFD alphasatellites, a different and smaller DNA was identified using rolling circle amplified DNA from CFDV virions (Table  S2 ). The molecule of 641 nt has no similarity with any sequence currently in GenBank and bears ORFs in both orientations (Table  1  and Fig. 4 ). Curiously, this DNA has a second origin-like inverted repeat sequence at nts 396-423 flanking the nonanucleotide CAGTATTAC in (-) orientation (Fig. 3 ). There is no information about the polarity of the strand that is encapsidated or on the sequence that may act as replication origin.
(a) The PhyML 63 tree was rooted using the BBTV DNA-R sequence (S56276). Branch support (% bootstrap) is indicated. Nodes with <70% bootstrap support were collapsed. Branches are coloured according to clustering of the alphasatellites. Red: coconut foliar decay alphasatellites; orange: babuvirus alphasatellites (incl. CFDA3 and CFDA6); brown, ochre, green: alphasatellites associated with begomoviruses and those isolated from insects; olive, violet, blue: nanovirus-associated alphasatellites. Names are according to  25  and GenBank accession numbers are indicated. (b) A pairwise DNA sequence comparison plot by SDT with % identity shown as a multicolour heat map  61. Only DNA-S. 1, DNA-gamma and CFDAR were detected in each sample. Two combined samples of 1988 from three Vanuatu hybrid coconut palms contained all ten DNAs (Table  2 ).
No sequence variation over a time span of 26 years was observed for CFDV DNA-gamma. Applying high throughput DNA and RNA sequencing to search for CFD-associated DNAs, only the three types of molecules identified earlier were uncovered: alphasatellites, DNA-S and DNA-gamma. Two new and distinct alphasatellites (CFDA5 and CFDA8) were first found by deep sequencing. Subsequently their physical presence in several samples of 1988/89 was proven by PCR and cloning. Hence, deep sequencing and amplification using component-specific primers yielded consistent data about the presence or absence of a given CFD-associated DNA in the samples analysed (Table  2 ). No sequences of other ssDNA-or RNA viruses and viroids were identified in DNA and RNA from CFD-affected palms.
CFDV DNA-gamma has no similarity with these deltasatellites and lacks an A-rich or satellite conserved region but, like the tomato leaf curl deltasatellite (ToLCD), it has a second potential stem-loop sequence  45. It bears small ORFs on each strand with respective coding capacities for small proteins of 9. 5 kDa (plus polarity) and 11. 5 or 11. 1 kDa (minus polarity), respectively. There is no significant similarity with sequences in GenBank. Given the apparent very high abundance of DNA-gamma in CFD-affected palms and its presence in all samples tested we consider DNA-gamma to be an integral component of the CFDV genome. The fact that DNA-gamma is almost precisely half the size of the other CFD-associated DNAs probably reflects the packaging constraints of the CFDV capsid: a DNA-gamma dimer would easily become encapsidated.
Furthermore, having been able to de novo assemble a CFDV DNA-S. 2 molecule from 0. 002% total RNA reads (219 of about 9. 7 million reads; Table  3 ) illustrates the sensitivity of our searches. Moreover, the deep sequencing of RNA, which allows detection of RNA and DNA viruses  52  , did not uncover any RNA virus associated with CFD. Among the multitude of circular replication-associated protein encoding single-stranded (CRESS) DNA viruses there is an example of a somewhat similar case to CFDV, the Pacific flying fox faeces associated multicomponent virus-1 (PfffaMCV-1)  53. The virus has a Rep-encoding DNA, a CP-encoding DNA, and a DNA encoding a potential protein with no similarity to any protein in the database. Like CFDV DNA-S. 1, CFDV DNA-gamma and CFDAR these three PfffaMCV-1 DNA types share only common sequences flanking the inverted repeat and the nonanucleotide at the replication origin.
32 g/ml) were pooled and denatured prior to analysis by 3-13% discontinuous SDS-polyacrylamide gel electrophoresis (SDS-PAGE)  57. Proteins were detected by silver staining, and the M r of the capsid protein determined by comparison with co-electrophoresed marker proteins. For identification by LC-MS/MS virions of ten samples collected in 1988 and 1989 (samples 2, 4, 5, 6, 7, 8, 10, 22, 23 and 29, Table  S1 ) in which no DNA-S. 2 was detected, were pooled, denatured and proteins separated by 15% SDS-PAGE. After staining by Coomassie brilliant blue the major protein band of ~24 kDa was excised, digested by trypsin and analysed by nanoLC-MS/MS as described  58. Protein identification was performed using the Mascot database search engine (Matrix Science, London, UK) against the CFDV-CP1 sequence with trypsin specificity and two missed cleavages.
). The sequencing library was prepared with the Nextera XT Library Kit (Illumina) and run after quality check on Illumina MiSeq as paired end reads (2 × 301 bp) (DSMZ, Germany). Sequence analysis. Sequences of cloned CFD DNAs were analysed with DNASTAR Lasergene, (v 12. 1) (DNASTAR, Inc. , Madison, WI). Consensus sequences of a given CFD DNA component were derived from at least three sequences of cloned DNA. Primary contigs (nodes) assembled by SPAdes 59 from the Illumina reads were further assembled using SeqMan Pro of DNASTAR or Geneious (v 8). Guided assemblies were done with SeqMan Pro, Geneious and CLC Genomics Workbench software (v 8. 0). Since SPAdes had produced too many obviously misassembled contigs (only DNA-gamma and DNA-S. 1 could be de-novo assembled from the SPAdes produced contigs), the single reads (17,427,262 from the CFD_1988/89 sample and 23,513,930 from the CFD_2013 sample) were directly assembled into contigs using Geneious v10.
2. 3. In the same way all single reads were mapped against the sequences of the cloned RCA products using Geneious v10. 2. 3. Unmapped reads (Geneious or CLC) were reassembled, and the resulting contigs were checked by BLAST for known virus sequences and obvious contamination by plant, microbe or human sequences. Phylogenetic analyses were conducted in MEGA7 60 and SDT v. 1. 2  61. Multialignments were done using Muscle  62  as implemented in Geneious or MEGA7. A maximum likelihood tree (100 bootstrap repetitions) was constructed by PhyML  63  with the GTR + G + I substitution model, chosen after model test in Mega7. BBTV DNA-R (GenBank acc. no. S56276) served to root the tree, and nodes with less than 70% bootstrap support were collapsed using Dendroscope, v3. 5. 8  64. The final graphics were done in FigTree v1.
4. 3. (http://tree. bio. ed. ac. uk/ software/figtree/). A recombination analysis was carried out using the recombination detection package RDP4  26. CFDV replication assays in plant leaf discs. Viral DNA replication was assayed in leaf discs of Nicotiana benthamiana, Hibiscus rosa-sinensis (var. Valencia) and Hyacinthus orientalis essentially as described previously  31. For replication assays, redundant copies (direct repeats) of CFDV components were constructed in the binary vector pBin19 (see Table  S6  for construction details) and transferred into Rhizobium radiobacter, formerly Agrobacterium tumefaciens, strain LBA 4404 by electroporation. Six days post inoculation total DNA was isolated from the leaf-disc tissue, fractionated on 1% agarose gels and transferred onto Hybond-N membrane (Amersham).
Acknowledgements We gratefully acknowledge support by Director and Staff of the  IRHO-CIRAD Station, now VARTC, Saraoutou, Vanuatu. J. W. R. is indebted to  J. -F. Julia  and  D. Hanold , and was supported through the  Australian Centre for International Agricultural Research. B. G. and T. T. were supported by  CNRS. Q. B. was in receipt of a PhD fellowship from the  Université Paris-Sud. The work has benefited from the facilities and expertise of the SICaPS Proteomic platform of I2BC. We thank  R. Briddon  and  A. Varsani  for providing unpublished information.
We identified another previously described site-1 mAb from others with similar affinity (clone 1A11 from WO/2011/094259 with a KD of 6 × 10 -10 M) that we recombinantly expressed with a human IgG1 Fc isotype as being developed in the clinic (NCT02293161). Analysis of conformational epitope using hydrogen deuterium exchange with mass spectrometry (HDX-MS) confirmed previous observations on linear epitopes and demonstrated that the site-1/2b mAb protected from deuterium incorporation in several peptides of the site-1 but also to a peptide overlapping the site-2b, while the two other mAbs (clone 1A11 and our site-1 IgG4 mAb) significantly prevented deuterium incorporation only in peptides from site-1 (Fig. 3a, b ). We then studied the impact of these confirmed site-1 and site-1/2b mAbs on STAT5, PI3K and ERK signaling pathways previously associated with IL-7R signaling.
b CD25 + (upper) and CD69 + (lower) activated T-cell frequencies at the indicated time-point in the same animals as in (a), after ex vivo culture (48 h), without stimulation or with anti-CD3 polyclonal stimulation, and supplemented with human IL-2 (300 UI/mL) or human IL-7 (10 ng/mL) as mentioned. c Oxygen consumption rate (OCR) and extracellular acidification rate (EACR) of T cells purified one week before and after anti-IL-7Rα treatment in the same animals as in (a). OCR and EACR was determined on freshly isolated and unstimulated T cells or after over-night polyclonal activation using Seahorse XF24 Analyzer. d ATP concentration (µg/mL) and mean fluorescence intensity (MFI) of 2-NBD glucose uptake in the same condition as in (c). Data are mean ± SEM not clearly affected by site 1/2b Ab, was reported to prevent TH17 polarization  51  , therefore it might be conceivable that some antiinflammatory actions of IL-7 are differentially inhibited by the two classes of anti-IL-7R mAbs and might contribute to the difference observed in vivo.
In contrast to most studies performed in rodent models where IL-7R blockade induce broad lymphodepletion  37  , administration of high doses (i. e. , 10 mg/Kg) of anti-IL-7Rα mAb targeting either site-1 or site 1/2b in non-human primates (here in baboons or previously by others in marmoset  42  or cynomolgus monkey  47  ) did not induce lymphopenia or significant decrease in peripheral T lymphocyte numbers. Similarly, early clinical results from phase 1 trials with two different site-1 anti-IL-7Rα mAbs in healthy volunteers (GSK2618960, NCT02293161) or in type 1 diabetic adult patients (PF-06342674, NCT02038764) did not report induction of lymphopenia (https://www. gsk-clinicalstudyregister. com/files2/gsk-200902-clinical-study-result-summary. pdf)  60. Thus, if IL-7 has been well-described in maintaining the pool of peripheral naive and memory T lymphocytes in mice, in primates, however, the importance of IL-7 in maintaining peripheral T-cell homeostasis is less evident and/or redundant mechanisms might explain the difference between species.
2% formic acid in acetonitrile (pH 2. 5) for 10 min at a flow rate of 40 µl/min at 0. 0 °C. Mass spectrometry analysis was performed on a Waters Xevo G2-XS ESI-Q-TOF mass spectrometer in the positive ion mode, with lockspray correction. Mild source conditions (temperature: 90 °C, capillary voltage: 2. 5 kV, sampling cone: 30 V, desolvation gas flow: 800 L/h, desolvation temperature: 250 °C) were used in order to minimize back-exchange while ensuring proper desolvation  65. Peptide identification was assisted by collision induced dissociation collected in the MSE mode, using PLGS 3. 0. 2 and UNIFI 1. 8. Deuterium incorporation was determined in DynamX 3. 0. Structural figures were prepared using PyMOL 1. 8. 2. 3 (Schrödinger LLC, Cambridge, MA, USA) from PDB ID 3DI3  17. Monobasic and dibasic sodium phosphate, sodium chloride, guanidine hydrochloride, Tris(2-carboxyethyl)phosphine hydrochloride (TCEP), 50% sodium hydroxide, and formic acid were purchased from Sigma Aldrich (Schnelldorf, Germany) at the highest available purity.
Data was separated by barcode and aligned using Tophat version 2. 0. 10 with default settings. Transcripts were quantified by the Broad Technology Labs computational pipeline using Cuffquant version 2. 2. 1  67. Briefly, data were processed through CuffNorm if 50% of the reads aligned, and if at least 100,000 pairs were aligned per sample. Normalization used the default settings, including "geometric" normalization, and expression level information as log2-transformed FPKM values (Fragments per kilobase of transcript per million mapped fragments) were used for subsequent analyses. For identification of differential genes, linear modeling with estimation of the mean-variance relationship (limma-trend) with empirical Bayes statistical procedure were performed using the limma package in R  68.
Genes with Benjamini and Hochberg adjusted p-value < 5% and fold change (FC) > 1. 5 were considered as differentially expressed. For gene expression representation, PCA and clustering were performed in R v3. 3. 2 using ade4/adegraphics and pheatmap packages respectively. The biological significance of selected genes was assessed using the R clusterProfiler package. Gene ontology (GO) categories enriched with a false discovery rate (FDR) < 5% and with at least five represented genes were selected. RNA-seq data have been deposited in GEO under the accession code GSE103643. Tuberculin-induced DTH model. Baboons were immunized intradermally twice with a BCG vaccine (0. 1 ml; 2-8 3 105 CFU; Sanofi Pasteur MSD, Lyon, France) in the upper region of the leg, 4 and 2 weeks before the DTH skin test.
Intradermal reactions (IDR) were performed with duplicate 0. 1 ml intradermal injections of two doses (2000 or 1000 IU) of tuberculin-purified protein derivative (PPD; Symbiotics Corporation, San Diego, CA, USA) in the skin on the right back of the animals. Saline injections (0. 1 ml) was used as a negative control. Dermal responses at the injection sites were measured using a caliper square. The diameter of each indurated erythema was measured by at least two observers from day 3 to 12, and was considered positive when above 4 mm in diameter. The mean of the reading was recorded and plotted for each time point. To compare multiple experimental conditions, erythema responses were quantified as area under the curve (AUC) using Graph Pad Prism software for calculation. Skin biopsies were performed on day 4 on one duplicate.
An anti-human CD127 (A019D5, dilution 1/10), and CCR7 (G043H7, dilution 1/5) were purchased from Biolegend. Anti-PD-1 (eBioJ105, dilution 1/10) was purchased from eBioscience, anti-human CD14 (TUK4, dilution 1/10) and anti-human CD33 (AC104. 3E3, dilution 1/10) from Myltenyi and anti-human NKp46 (BAB281, dilution 1/10) from Beckman Coulter. Samples were acquired on a BD FACS LSRII flow cytometer (BD Biosciences) and analyzed with FlowJo software. The percentage of receptor occupancy (RO), was determined using flow cytometry staining with a non-competitive commercial anti-human CD127 mAb (hIL-7R-M21) and a competitive commercial anti-human CD127 mAb (A019D5). The percentage of free CD127 + cells in total CD127 + T cells was analyzed by flow cytometry. Elispot assays. Baboon PBMCs were prepared from whole blood by Ficoll gradient centrifugation (GE Healthcare Life Science, Paris, France).