dataesr/scientific-paragraphs-categorization huggingface dataset:
The sequences were manually corrected for several frameshifts in IL_B6, IL_C4, IL_F5 and IL_D12. Annotations of putative proteins were performed by homology searches using the Blast facilities against Reference Protein Sequences database and were validated using tBlastN with the MetaHit 9. 9 M gene catalogue. Best hits are summarized in Supplementary Table  S2. EggNOG assignment was performed with 251 predicted proteins from hit clone CDS, including non-redundant proteins for either IL-F5/B6/B1/D12 or IL-D9/C4, using BlastP with the eggNOG 4. 0 database  61  (E-value ≤ 10 -7 , identity percentage ≥ 80%, best hit chosen). We assigned eggNOGs to members of the non-supervised orthologous groups of Bacteria, Bacteroidetes, Firmicutes, Bacteroidia and Bacilli. The functional category was assigned for 145 proteins with a BlastP result.
For the remaining unclassified (UC) CDS encoded proteins, 56% were short predicted proteins (< 150aa). For proteins with multiple eggNOG assignation, we have chosen the consensus category when possible, otherwise, the first one. The radial plot was made with R radial. plot function of the plotrix library  62. CAZYme annotation and PUL prediction. Carbohydrate related enzymes encoding genes were identified by Blast analysis of the predicted ORFs against the functional modules of all CAZyme groups (GH, PL, CE, GT and CBM) included in the Carbohydrate Active Enzyme database (http://www. cazy. org) using a cut-off E-value of 7. 10 -6 followed by visual inspection and alignment with known CAZy families  27  to validate the prediction with human curation. The presence of Polysaccharide-Utilization Locus (PUL) in metagenomic insert sequences was determined using Blast against protein datasets for species in the Polysaccharide-Utilization Locus Database (PULDB) at http://www.
9 million human gut microbiota reference genes, constructed using 1,267 fecal samples from European, Chinese and U. S. individuals  6. Homologs were selected using BlastP (E-value = 1e-05, identity percentage ≥ 80% and alignment length ≥ 90%). Taxonomic annotation of the hits found in the catalogue was performed on the corresponding genes using BlastN and the NCBI nt and WGS databases. Heat map was generated using the momr R package and the deposited 9. 9 M gene frequency matrix (http:// meta. genomics. cn/metagene/meta/dataTools). Microbial gene richness was measured by counting the number of genes identified in a given sample using 11 million reads as performed in the original studies  65.
: non classified. a clones partially redundant. The GH9, GH31 and GH9 of IL_D9 are identical to the first three GH of IL_C4. b clones partially redundant. Proteins from the same CAZyme family are identical in the corresponding clones. c clones partially redundant. The GH5_2 enzymes are identical. d Order, Family or genus assigment, according to BlastP analyses using the database Reference Protein Sequences (ref_seq_ protein). e Genbank accession number and PubMed-indexed for MEDLINE (PMID) are given for each best hit. Because the OS xylan was composed of 75% xylose, 10% arabinose and 15% glucose, the likely presence of xyloglucan or β -glucan polysaccharides could introduce false positives in the xylanase activity detection. However, none of the clone exhibited xyloglucanase activity in agar well-plate assays (not shown).
Acknowledgements This work was partly supported by a grant to BH: European Union's  Seventh Framework Program  ( FP/2007/2013 )/ European Research Council (ERC)  Grant Agreement 322820. OP was a recipient of a grant for doctoral research allocated by the French ministry of higher education and research (doctoral school 569 Paris-Saclay). This study is dedicated to the memory of  Florence Blon , engineer assistant of the FInE team who worked on GH with an admirable rigorous and efficiency and passed away in october 2014. We are grateful to the  INRA GenoToul sequencing platform  (http://www. genotoul. fr)which performed the DNA sequencing of the metagenomic inserts, and to the  INRA MIGALE bioinformatics platform  (http://migale. jouy. inra. fr)for providing computational resources. We are very grateful to  Marine Plestan  who performed transposition experiments on two metagenomic clones, during her master fellowship.
In the repeated exposure regimen, cell viability in the Caco-2 monoculture was assessed using the trypan blue exclusion assay. Viable and non-viable cells were counted using an automatic cell counter (Countess automatic cell counter, Invitrogen). Cytotoxicity was assessed for the Caco-2/HT29-MTX coculture model based on propidium iodide (PI) exclusion. Cells were incubated with PI before counting using a FacsCalibur analyzer (BD Biosciences) equipped with CXP software (Beckman Coulter). Mean fluorescence was analyzed using Flowing Software 2. 5. 1 (http://www. flowingsoftware. com/). In both exclusion A c c e p t e d M a n u s c r i p t assays, measurements were performed in triplicate for each condition; results are expressed as the mean percentage of viable cells after normalization relative to the untreated control.
Slides were cooled on ice, before immersion in cold migration buffer (NaOH 300 mM, A c c e p t e d M a n u s c r i p t 7. 4, then stained with Gel Red (VWR). %tail DNA was measured on 50 nuclei using Comet IV software (Perceptive instruments). As positive control for comet-Fpg, A549 cells were exposed to 1 µM riboflavin for 20 min at 37 °C and then UVA-irradiated (010. 0 J/cm²). As positive control for comet alkaline assay, control (unexposed cells) slides were exposed to 50 mM H 2 O 2. Experiments were performed in three independent replicates. Results were normalized for %tail DNA in control (unexposed) cells, and expressed as mean fold-change ± standard error calculated over the three independent experiments.
Acknowledgments This work was supported by the  French Atomic Energy and Alternative Energies Commission (CEA)  through the  'Toxicology' research program , the  French Environment and Energy Management Agency (ADEME) , the  French Agency for Food, Environmental and Occupational Health & Safety (ANSES)  within the framework of the  National Research Program for Environmental and Occupational Health  ( ANSES, Nanogut project ) [ EST-2013/1/024 ] and the  French National Research Agency (ANR ,  PAIPITO  project )  [ ANR-16-CE34-0011-01 ]. This study is a contribution to the  Labex Serenade  [ ANR-11-LABX-0064 ] funded by the  French Government 's  "Investissements d'Avenir" program  through the A* MIDEX  project [ ANR-11-IDEX-0001-02 ]. The authors would like to thank  T. Lesuffleur  ( INSERM U938, Paris, France ) for her generous gift of HT29-MTX cells, and  T.
Study design and population These analyses used data from the subcohort of the European Prospective Investigation into Cancer and Nutrition (EPIC)-InterAct study. EPIC-InterAct is a case-cohort study of type 2 diabetes nested within eight countries of the EPIC cohort study, namely France, Italy, Spain, UK, the Netherlands, Germany, Sweden and Denmark  [21]. Briefly, from the entire cohort of 340,234 participants with blood samples (baseline years, 1991-1998) in the eight countries, we ascertained incident diabetes cases and selected a random subcohort of 16,835 participants. Participants with prevalent diabetes at baseline were excluded (n = 681)  [21]. A further 235 participants with no available fatty acid data were also excluded. Thus, a total of 15,919 participants were included in this study.
Nine SFAs had a relative concentration higher than 0. 05%. Data quality was assessed using quality control samples across all of the batches, which showed that the SFAs and their coefficients of variation were C14:0 (9. 4%), C15:0 (11. 9%), C16:0 (1. 6%), C17:0 (4. 2%), C18:0 (2. 0%), C20:0 (15. 3%), C22:0 (10. 3%), C23:0 (18. 9%) and C24:0 (14. 7%). Serum metabolic markers were measured at Stichting Ingenhousz Laboratory (Etten-Leur, Netherlands), from samples stored at -196 °C (-80 °C in Umeå). These metabolic markers included lipid markers (total cholesterol (TC), HDL-C TG, apolipoprotein A-1 (ApoA1) and apolipoprotein B (ApoB)), liver function markers (alanine transaminase (ALT), aspartate transaminase (AST), gamma glutamyl transferase (GGT)), and an inflammatory marker (C-reactive protein (CRP)).
Diet and lifestyle measurements The assessment of habitual diet during the past 12 months was undertaken using self-or intervieweradministered, country-specific validated dietary questionnaires  [26]. Based on the standardised EPIC Nutrient Database  [27] , total energy and nutrient intake were calculated. At baseline, we used standardised health and lifestyle questionnaires to assess demographics, smoking status, medical history and educational level. Physical activity was assessed using a brief questionnaire at baseline, which divided participants into four physical activity groups, namely inactive, moderately inactive, moderately active or active  [21].
Acknowledgements We thank all EPIC participants and staff for their contribution to the study. We thank  Nicola Kerrison  ( MRC Epidemiology Unit, Cambridge ) for managing the data for the InterAct Project,  Matt Sims  for writing the technical laboratory specification for the intermediate pathway biomarker measurements and for overseeing the laboratory work, and  Laura Wang  and  Keith Summerhill  ( MRC Human Nutrition Research, Cambridge ) for the fatty acid measurements. We thank the technical and functional operational teams of the  MRC Epidemiology Unit  for enabling all biomarker measurements. Federico II, Naples, Italy. 26Escuela  Andaluza de Salud Pública, Instituto de Investigación Biosanitaria ibs. GRANADA, Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain.
RESULTS AND DISCUSSION The cnt operon of P. aeruginosa is regulated by zinc level through the zinc-responsive regulator Zur In silico analysis of the cnt gene cluster of P. aeruginosa PA14 strain indicated two overlapping open reading frames between cntL and cntM and between cntM and cntI, classically observed in operonic structures (Figure  S1 ). Further screening of the upstream cnt sequence for promoter regions using Bprom software  (23) , revealed a σ70 promoter in the 200 base-pairs upstream from the annotated cntO ATG codon (Figure  S1 ). Interestingly, a putative Zur binding box "GTTATagtATAtC" can be identified overlapping the -10 box of the predicted σ70 promoter,  (22, 24). This in silico analysis supports an operonic organization of the four cnt genes and strongly suggests a transcriptional activation of this operon under zinc depletion through the Zur repressor  (25, 26).
Pseudopaline is involved in nickel and zinc uptake, depending on the chelating properties of the media In order to address the involvement of pseudopaline in metal uptake in vivo, we compared the intracellular concentration of various metals in PA14 WT, ΔcntL and ΔcntL::cntL strains. Cells were grown in pseudopaline-synthesis conditions determined above (MS medium) and the intracellular metal concentration was measured by ICP-MS. Under these growth conditions we observed a significant 90% reduction of intracellular nickel concentration in the ΔcntL mutant strain (Figure  4A ), which was mostly recovered in the complemented strain. The levels of all the other metals were not changed in the ΔcntL mutant strain compared to the WT strain (data not shown). A similar 90% reduction in intracellular nickel concentration was also observed when the culture was supplemented with 1μM NiCl 2 (Figure  S4 ), thus confirming that nickel uptake was predominantly performed by pseudopaline in these metalpoor media.
ACKNOWLEDGEMENTS This work was supported by the  ANR-14-CE09-0007-03  grant allocated to PA, RV, RL and EBD and the grant from " Vaincre la Mucoviscidose " (RFI20160501495) allocated to RV and PA. We thank  B. Douzi  for fruitful discussions,  B. Ize  for RNA preparation and  C. Soscia  for technical support as well as  O. Uderso ,  I. Bringer  and  A. Brun  for material and media preparations.
Citrulline Concentration Fasting plasma citrulline concentration assay (μmol/L) was performed at day -30 by high-performance liquid chromatography method (Shimadzu C18 column, Kyoto, Japan) along with tandem mass spectrometry (AB Sciex 3200 Qtrap, Framingham, MA) using the aTRAQ kit for amino-acid analysis of physiological fluids (AB Sciex)  [13]. Acquisition in the mass spectrometer was achieved by multiple reaction monitoring. Data recording and analysis were performed with Analyst software, v. 1. 6 (AB Sciex).
Cytokine Assay Supernatant (50 μL) was thawed to assess levels of TNFα, IL-1β, IL-6, IL-10, and INF-γ by use of Luminex microbead method (R&D System, Minneapolis, MN; detection sensitivity was as low as. 4 pg/mL to 1. 7 pg/mL). These cytokines had been searched for according to accountability for aGVHD pathophysiology  [17]. INF-γ was assessed to confirm the absence of lymphocytes in cell culture. For each patient, all stimulation assays were simultaneously assessed on a 96-well plate. Data were acquired by multiplex cytokine Bio-Plex Manager (Bio-Rad Laboratories, Marnes-la-Coquette, France) and analyzed by xPONENT software (Luminex, Austin, TX). ELISA kits were used according to manufacturer's protocol to validate analyses (eBioscience, San Diego, CA). Monocyte-derived macrophages were considered viable when LPS-induced TNF-α releasing was greater than 100 pg/mL  [9, 18].
ACKNOWLEDGMENTS This study was supported by grant from Nutricia Nutrition Clinique on behalf of the Société Francophone Nutrition Clinique et Métabolique (SFNEP) awarded to Thomas Hueso in 2014. The authors thank the staff of the hematology department of the University Hospital of Lille, France, for patients' recruitment and blood sample collection. The authors also thank the department of biochemistry for amino-acid analyses and the Lille Inflammation Research International Center of UMR 995 Inserm for material support. The authors acknowledge Caroline Dendoncker, dietetician, for patient care, Rachid Aijjou, for technical help, and Laura Ravasi, MD, PhD, for her assistance in writing and English editing the manuscript. The authors also thank Noël Milpied MD, PhD for critically reviewing this manuscript.
Preparation of recombinant PrP constructs Full-length Ovine PrP 23-234 (Ala-136, Arg-154, Gln-171 variant) were produced in Escherichia coli and purified as described previously  [9]. The O1 oligomers were generated by incubating of OvPrP at 80mM at 55˚C for 6 hours and purified as previously detailed  [4]  by size exclusion chromatography (SEC). SEC experiments have been performed using TSK 4000 SW column equilibrated with Sodium citrate 20mM pH 4. 0 coupled to an AKTA Purifier 100 (GE-HealthCare). The size distribution of O1 assemblies was estimated by coupling to multiwavelength static light scattering with size exclusion chromatography using a TSK 4000SW. The resulting data were transformed to size distribution using a custom MATLAB program. The depolymerisation of O1 assemblies was followed by static light scattering (SLS) by incubating O1 assemblies at 50˚C.
Mathematical description of measured quantities In the following we provide a mathematical description of the quantities measured by SLS and SEC devices. Thanks to these formulas we can compare our qualitative model to the experimental data. The SLS data (Fig 2A, 2B and 2C) measure an affine transform of the mean average molecular weight < Mw >, which corresponds mathematically to the second moment of the distribution. Denoting SLS(t) the measurement by the SLS device at time t, we have that there exist two constants such that SLSðtÞ ¼ cðmðtÞ þ X 1 i¼2 i 2 o i ðtÞÞ þ c 0 ; ð1Þ where m is the concentration of isolated monomers, o i is the concentration of oligomers composed by i monomers, and (c, c 0 ) are two unknown positive constants depending on the experimental setting. We detail in S2  The separation of O1 assemblies from the other type of assemblies and monomer has been performed using size exclusion chromatography coupled to multiwavelength static light scattering lead to estimate size of oligomers generated during PrP oligomerisation.
Parameter identification based on Kalman estimation To estimate the four parameters k on , k dep , k dis and y ¼ o a i ð0Þ o a i ð0Þþo b i ð0Þ , we rely on an Extended Kalman Filter (EKF) approach  [10]  implemented in MATLAB. In order to apply the EKF, we need to define a complete dynamical system including the parameters to be estimated. To this end, the variables o b i are substituted by their analytical expressions o b i ðtÞ ¼ e À k dis t o b i ð0Þ ¼ e À k dis t o b i 0. We consider the state variables o a i , o b i 0 and m, extended with the parameters k on , k dep and k dis with a null dynamics d dt k on ¼ 0; d dt k dep ¼ 0; d dt k dis ¼ 0: We also need to define an a priori of the initial state that would be the initial condition of the EKF estimator. Direct model simulations allowed us to define the a priori values k on 0 ¼ 0:031 min À 1 mM À 1 , k dep 0 ¼ 0:09 min À 1 , k dis 0 ¼ 0:07 min À 1 , θ 0 = 0.
Data We used data from Cambodia Demographic and Health Surveys (CDHS) conducted in 2000, 2005, 2010 and 2014 to collect information from a nationally representative sample on household demographic and socio-economic characteristics and on child anthropometry, child feeding practices and child health. Women aged 15-49 years responded to a specific questionnaire that comprised questions on the total number of children born to them and maternal birth history. Birth history questions included date of birth for every live birth, survival status, current age of surviving children and age at death for those deceased. Because neonatal mortality is a rare event, live births that occurred during the ten years prior to the date of interview were included in order reach an adequate sample size. CDHS were based on stratified samples selected at two stages, and each reporting domain was separated into rural and urban areas.
Finally, quadratic terms were included in the model when we found a U-shaped relationship between NMR and a confounder. Tracking changes in inequality. To summarise changes in absolute and relative inequities in NMR over time, we calculated the absolute mean annual changes of the inequality measure between the last survey and the three others. Trends were assessed calculating the mean annual change of the inequality measures for three time periods. For graphical purposes, we show annual changes in relative inequality on a log-scale because it allowed a symmetry around zero. All analyses took into account the sampling design (stratification, clustering, sampling weights) and were conducted using Stata (version 13. 0) and R (version 3. 3. 1) software.
Griptite Cell Culture and Experiments Griptite cells were cultured and transfected with 3 µg DNA (either ASBT in pCMV plasmid or empty pCMV control plasmid) similarly to HEK cells, as previously described  [20, 21]. Transfection efficiency was verified by western blotting, as previously published  [22]. A pre-incubation of the cell monolayers with DMEM supplemented with either DMSO (control) or 100 µM simvastatin was performed during 30 min. Synthetic mixed micelles containing vitamin D forms were diluted in DMEM (1:5) to avoid cytotoxicity  [23] (data not shown). Apical uptake of vitamin D forms was determined after a 1 h-incubation with a solution of micellar vitamin D containing either DMSO or 100 µM simvastatin (final concentration of DMSO in both conditions: 0. 01%)  [20, 21]. The % of vitamin D taken up was estimated as the quantity of vitamin D present in the harvested cells divided by the sum of the quantity of vitamin D remaining in the apical chamber and that present in the harvested cells.
Statistical Analysis Data were expressed as means ± SEM. Differences in Vitamin D form micellar incorporation and cellular uptake and efflux were tested using ANOVA (fixed-effects models). Prior to ANOVA, data were tested for equality of variances. Tukey's test, which maintains the family-wise error rate at alpha = 0. 05, was used as a post hoc test for pairwise comparisons. Student's t-test was used to test the effect of membrane protein inhibition on the different form uptake. Data were tested for equality of variances and in case of inhomogeneous variances, Welch's correction was applied to Student's t-test. Values of p < 0. 05 were considered significant. Statistical analyses were performed using SPSS (version 20, SPSS Inc. , Chicago, IL, USA).
Statistical Analysis Data were expressed as means ± SEM. Differences in Vitamin D form micellar incorporation and cellular uptake and efflux were tested using ANOVA (fixed-effects models). Prior to ANOVA, data were tested for equality of variances. Tukey's test, which maintains the family-wise error rate at alpha = 0. 05, was used as a post hoc test for pairwise comparisons. Student's t-test was used to test the effect of membrane protein inhibition on the different form uptake. Data were tested for equality of variances and in case of inhomogeneous variances, Welch's correction was applied to Student's ttest. Values of p < 0. 05 were considered significant. Statistical analyses were performed using SPSS (version 20, SPSS Inc. , Chicago, IL, USA).
Densitometric analysis of PrP Sc Western blot data Semi-quantification of PrP Sc levels was performed using a GS-800 calibrated densitometer and Quantity One software (Bio-Rad Laboratories). Values for the three PrP Sc glycoforms were measured on blots with a nonsaturated signal as described  (10, 38). When the signal was saturated, the amount of PrP Sc was measured on the last quantifiable dilution (y). The final value (PMCAϩ) was obtained using the formula: (y) ϫ dilution factor as described  (36). For each studied region, we calculated the amplification of PrP Sc signal by PMCA as follows: amplification region ϭ ((PMCAϩ) Ϫ (PMCAϪ))/(PMCAϪ). The relative amplification region was calculated as a function of the value of the internal standard of amplification contained in each experiment (amplification standard ): Relative amplification ϭ amplification region /amplification standard.
Statistical analysis For statistical comparisons between regions, and according to the sample size, the nonparametric Mann-Whitney test was used. For correlations between in vivo regional targeting and in vitro PMCA results the Pearson test was used. Analyses were performed using Statview Software version 4. 0 (Abacus Concepts) and SigmaStat software version 3. 5 (Systat Software). Data are presented as the mean Ϯ S. E. , p Ͻ 0. 05 was considered to be statistically significant. Author contributions-N. P. was the primary experimentalist. S. H. designed the study. N. P. , E. L. , Sa. H. , and S. Y. performed experiments. J. -L. L. performed PRNP genotyping. V. B. and S. H. performed mouse inoculations. D. S. , J. -P. B. , and S. H. contributed to the clinicopathological analysis. All authors participated in analyzing and interpreting data and contributed to the manuscript.
Experimental Conditions for Metabolic Responses and Glucose Kinetics Blood samples were taken at baseline (before eating breakfast) and then regularly during the postprandial period (9 to 17 samples), as described in  Vinoy et al. (2013)   [30]. Glucose and insulin concentrations were measured for each blood sample. The glycemic responses were followed for 270 min after the subjects began to consume breakfast. RaT and RdT were calculated from plasma D-(6,6-2 H 2 ) glucose enrichment, and RaE and RdE were determined from plasma ( 13 C)-glucose enrichment  [29] [30] [31] , as described previously  [34]. When the design of the studies was taken into account (parallel or cross-over, and the number of test products per subject), there were 126 and 152 data points available from the isotope and metabolic response experiments, respectively.