dataesr/scientific-paragraphs-categorization huggingface dataset:
Vitamin D and retinyl acetate (Sigma Aldrich) were separated using a 250 × 4. 6 nm, 5 µm Zorbax Eclipse XDB-C 18 column and a guard column (Agilent). The mobile phase was 60% acetonitrile, 38% methanol and 2% water. Flow rate was 1. 5 mL/min and the column was kept at a constant temperature (40 • C). Vitamin D was identified by spectral analysis and/or on the basis of the retention time and co-injection compared with the pure standards. Quantification was performed using the Chromeleon software (version 6. 8, ThermoFisher Scientific, Villebon sur Yvette, France) by comparing the peak area with the standard reference curves. All HPLC-grade solvents were from Carlo-Erba (Peypin, France). Vitamin D bioaccessibility was calculated as the percentage of vitamin D recovered in mixed micelles relative to the amount of vitamin recovered in the whole digesta at the end of the digestion.
Elution was carried out with a heptane/ether/formic acid mixture (55:45:1, v/v/v) for approximately 20 min. The chromarods were then dried and solvent evaporated in an oven at 150 • C for 15 min. The detection was carried out using a Iatroscan MK6 device (Iatron laboratories), and chromatograms were integrated using the Chromstar software. Mass detection data were converted in moles using calibration curves established with various amounts of oleic acid, monoolein, diolein and triolein, used as reference standards. The lipolysis level was expressed as the percentage of free fatty acids (FFA) and monoglycerides present at the digestion end relative to the total amount of acyl chains present in the test meal triglycerides.
3 mM Tris, 2 mM CaCl 2 , 150 mM NaCl and 0. 5 mM or 4 mM sodium taurodeoxycholate. Several concentrations of the bioactive compounds were tested. A stock solution of pancreatin at 10 mg/mL was prepared in pure water, and 3 µL were used for each assay, with 5 μL of colipase (1 mg/ml) that is required to measure the full enzyme activity in the presence of bile salts. Purified bioactive compounds were added during the pHstat test. Three attempts were made to study the inhibitory effect of each compound, and different concentrations of each compound were tested. Their concentrations were chosen to represent those present in pulses, according to previous data  (Margier et al. , 2018).
Statistical analysis Results are expressed as the mean ± SEM. Differences between more than two groups of unpaired data were tested using the non-parametric Kruskal-Wallis test. The non-parametric Mann-Whitney U test was used as a post-hoc test when the Kruskal-Wallis test showed significant differences among groups. P values ≤ 0. 05 were considered significant. All statistical analyses were performed using the GraphPad Prism software,.
Lipolysis is delayed in the presence of chickpeas, partly due to inhibition of the pancreatic lipase activity Lipolysis rate reached 32. 2 ± 3. 5% at the end of the in vitro digestion of chickpeas, and 47. 7 ± 6. 5% at the end of the in vitro digestion of semolina (data not shown). Pancreatic lipase activity was then inhibited by addition of different bioactive compounds during the lipolysis reaction (Fig. 3 ). First, the effects of these compounds were measured when the lipase was in the presence of colipase and 0. 5 mM bile salts, the optimum concentration for measuring pancreatic lipase activity. Indeed, higher concentrations could have concealed the inhibitory effects of bioactive substances. Then, the inhibition assays were repeated in the presence of 4 mM bile salts, a micellar concentration that allows displacing surfactants from the oil-water interface.
Acknowledgments This work was funded by a national Priority  Action of the Human Nutrition department of the French National Institute for Agriculture, Food and Environment (INRAE). T. Antoine received a doctoral fellowship from  INRAE ,  CTCPA  and  C2VN. Authors are grateful to  Marielle Margier  ( C2VN, Marseille, France ) for helpful technical help. This work was partly presented as a poster at the 13th European Nutrition Conference, October 15-18 2019, Dublin (Antoine et al. , 2020).
in 1974   1. This notion has gained strong support by the recent discovery of lytic polysaccharide monooxygenases (LPMOs) that uniquely catalyse the oxidative cleavage of glycosidic bonds in (semi)crystalline polysaccharides such as starch  [2] [3] [4]  , chitin  5  , cellulose  [6] [7] [8]  and cellulose-bound hemicelluloses, e. g. , xyloglucan  9  and xylan  10. Besides LPMOs, filamentous fungi co-secrete an impressing diversity of carbohydrate-specific oxidoreductases  11. To date, only four fungal oligosaccharide-oxidising enzymes from the auxiliary activity family 7 (AA7) in the Carbohydrate Active enZyme (CAZy) database  12  , have been characterized. In addition, oligosaccharide oxidases from plants have been reported  13, 14  , but are currently not assigned into AA7. Our insight is, thus, clearly limited regarding the biological roles as well as the diversity of substrates and redox features within this family.
Methods Bioinformatics and phylogenetic analysis. The sequences of 2200 putative AA7 sequences were retrieved by a BlastP search against the non-redundant protein database interfaced the NCBI server (https://blast. ncbi. nlm. nih. gov/Blast. cgi) using the FgChitO sequence (Genbank accession: XP_011325372) as a query and default search settings. The retrieved sequences were filtered by excluding noneukaryotic proteins and those displaying <25% amino acid (aa) identity and <90% coverage to the query. Two additional AA7-like sequences, which were differentially upregulated in the secretome of Aspergillus nidulans grown on starch  31  , and a longer sequence possessing an N-terminal extension of about 250 amino acid residues (aa) (MoChi7A) were also included in the sequence inventory. Only sequences comprising 470-570 aa (n = 1927) were aligned using MAFFT  51  with default parameters, and curated using Gblock0.
Manual model rebuilding and map inspection were performed in Coot  59  and analysed using MolProbity  60. The final validated structural models of FgCelDH7C and FgChi7B were deposited to the Protein Data Bank under the entry codes 6YJI and 6YJO], respectively (Data collection and refinement statistics are in Supplementary Table  4 ). Cellulose degradation assays based on the interplay between LPMOs and AA7 enzymes. The assays were performed using suspensions of either 1% PASC  61  and/or 0. 5% Avicel (Honeywell Fluka, Morris Plains, NJ, U. S. A) (both w/v) in 250 or 500 µL containing 4. 4 µM of PaLPMO9E 20 , PaLPMO9H 20 or LsAA9A 35 as well as 0. 4 µM FgCelDH7C (0. 2 μM in case of LsAA9A) in 50 mM NaOAc, pH 5. 2 in the presence of cellotetraose (DP4, 0. 8 mM), unless stated otherwise. For the comparison of FgCelDH7C and MoChi7A, 0.
The solubilised oxidised and non-oxidised oligosaccharides, released by the enzymatic treatments, were analysed by high-performance anion-exchange chromatography coupled with pulsed amperometric detection (HPAEC-PAD) (ThermoFischer Scientific) using a CarboPac™ PA1 (ThermoFischer Scientific) and a CarboPac™ PA1 guard column (2 × 50 mm) at 0. 25 mL min -1 and an eluent system as described by Westereng et al. 62. The Chromeleon 6. 80 SR10 software was used to interface the instrument and analyse the chromatograms. Non-oxidised oligosaccharides were used as standards (Megazyme, Wicklow, Ireland), whereas the corresponding C1-oxidised standards (from DP2-DP6) were provided from native cello-oligosaccharides using PaCDHB treatment  34. EPR spectroscopy. EPR experiments were performed on a Bruker ELEXSYS E500 X-band spectrometer equipped with an ER4102ST standard rectangular Bruker EPR cavity fitted to an Oxford Instruments ESR 900 helium flow cryostat.
Acknowledgements This study was supported by a  Novo Nordisk Foundation  Post-doc grant within the  Biotechnology Based Synthesis and Production Research Programme  to MHM ( NNF17OC0025642 ). F. F. and D. H. W. were funded by The  Novo Nordisk Foundation  Grant No. NNF10CC1016517. NMR spectra were acquired at the NMR center  DTU  supported by the  Villum and Carlsberg Foundations. J. G. B. , B. G. (Bruno G) and F. B. (Frédéric B) thank  IM2B  ( Institut de Microbiologie, Bioénergies et Biotechnologie ). The DSC instrument is funded by the  Carlsberg Foundation  Grant ( 2013-01-0112 ) to M. A. H. The authors are also grateful to the  EPR  facilities available at the  French EPR network  ( IR CNRS 3443 ) and the  Aix-Marseille University EPR center. Prof. Peter Westh  and  Dr. Jeppi Kari  are acknowledged for discussion on the redox-activities of  AA7.
Data availability The atomic coordinates of FgCelDH7C and FgChi7B have been deposited in the Protein Data Bank (https://www. rcsb. org) under the PDB accessions 6YJI and 6YJO, respectively (see also Supplementary Table  4 ). The GenPept accession IDs of the enzymes characterised in the study are given in Supplementary Table  1. All the data are available from the corresponding authors upon request. Source data are provided with this paper.
Findings: With 973,869 HC measurements from 157,762 children, new calibrated HC growth charts from birth to age five years were generated. The new HC growth charts showed good external fit by comparison with the ELFE birth cohort. As compared with the new HC growth charts, the previous French and WHO growth charts mean HC z-scores were, respectively, -0. 4 and -0. 6 SD for girls and -0. 2 and -0. 6 SD for boys. Interpretation: We produced and validated national calibrated HC growth charts by using a novel big-data approach applied to data routinely collected in clinical practice. Comparison with previous French and WHO growth charts confirmed a positive secular trend since the 1960s and regional specificities.
Derivation of new HC growth charts We used a two-step multicentre longitudinal design. First, we automatically extracted data for individual paediatric patients from electronic medical records fulfilled by primary-care physicians; we combined these data in a secured medical observatory dedicated to research and accredited for data health storage. Second, tens of thousands of extracted HC measurements were analysed. This approach has been described in detail elsewhere for the derivation of height and weight growth charts  [26]. The study protocol was approved by the ethics committee and institutional review board of the French Institute of Medical Research and Health (Inserm IRB00003888, IOR0003254, FWA00005831), which provided a waiver of consent given the completely anonymous design of data collection.
We included all children up to age five years who were born after 1990 with birth weight > 2500 g and who were measured at least once by their primary-care physician. Participating physicians belong to one of two participating primary-care medical societies (French Association of Ambulatory Pediatrics or French Society of General Medicine) and had to use the last version of the same electronic medical-records software. We recruited 32 randomly sampled primarycare paediatricians after stratification by geographical area and size of urban area (i. e. , four participants for each of the eight Research and National Development zones-two in large urban areas and two in small urban areas), and 10 volunteer general practitioners (Supplementary Figure  1 ). Participating physicians had routinely entered data including sex, year of birth, HC and age at growth measurement into the electronic medical records between 1990 and 2018, and such data were automatically and anonymously extracted from their computers.
Implication of all the available evidence HC growth monitoring may be optimized by using these national calibrated HC growth charts generated from a big-data approach, based on data routinely collected in clinical practice. and compared models with the Generalized Akaike Information Criterion (Supplementary Box 1). HC growth charts were modelled until age five years because the number of measurements after this age was insufficient to allow a good fit of the model and good accuracy of the growth charts. Furthermore, the clinical interest of HC monitoring after age five years requires additional evidence  [5, 29]. The internal fit of the final model was checked by inspecting empirical SD values and worm plots  [30]. Empirical SD values were calculated by grouping data by 3-month intervals. Worm plots were represented by two-month intervals from birth to six months, threemonth intervals from six to 12 months, six-month intervals from 12 to 24 months, and 12-month intervals from 24 to 60 months.
Thus, 16,873 children included in the ELFE birth cohort with 70,996 HC measurements from birth to 30 months were analysed. Data from the ELFE birth cohort, and previous French and WHO growth charts, as summarised in Supplementary Table  2 , were compared to new HC growth charts by converting HC values to z-scores based on the new HC growth charts  [32]. We assessed and represented graphically the mean HC z-score-for-age from birth to five years. We performed a visual comparison of the median and § 2 SD for the new HC growth charts with the ELFE birth cohort data and with previous French and WHO growth charts. All statistical analysis involved using R v3. 4. 2 (R foundation for Statistical Computing, Vienna, Austria) and GAMLSS package v5. 1. 2.
Main findings and interpretation We constructed and validated new national calibrated HC growth charts from birth to age five years with data for contemporary children. The HC of contemporary children was slightly greater than the one from previous French or WHO growth charts, which suggests a positive secular trend since the 1960s and regional specificities. This secular trend seemed to be more pronounced in girls and to narrow with age. Previous French growth charts had lower median and § 2 SD curves than the new HC growth charts, which indicates that children born in the 1960s had a smaller HC compared to children born in the 2000s, especially in the first two years of life. This gap between HC growth charts suggests greater HC prenatal growth and accelerated HC growth during the first year of life for children born in the 2000s as compared with those born in the 1960s.
Strengths and limitations With an automated approach, we produced updated and calibrated national HC growth charts from birth to five years by using a large and national contemporary sample. The growth charts were validated by comparison to a national population-based sample. This novel big-data approach applied to data routinely collected in clinical practice appeared to be less time-consuming and costly than classical ad-hoc cross-sectional surveys. However, some limitations deserve to be discussed. First, HC was less routinely measured by physicians as children become older. Unfortunately, we were not able to collect data allowing to compare the general characteristics of children measured or not after a certain age to explore potential selection bias. Second, the recruitment in primary-care phycisians might have introduced a potential selection bias by selecting children with higher socioeconomic status and better nutrition, which may overestimate the new national HC growth charts and limit their generalization to the French population.
This bias was limited by the additional recruitment of general practitioners  [26]. We did not collect any information on socioeconomic status, which prevented from better characterizing this potential bias. Third, data regarding any congenital or acquired condition affecting HC growth were not available. We addressed this limitation by excluding data for children with an excessive number of HC measurements and by applying a data-cleaning process. The empirical SD values for head circumference were calculated by grouping data by three-month intervals. The mean head circumference z-scores-for-age of data from the ELFE birth cohort are represented graphically by using spline curves. Note: a difference of 1 SD is equivalent to a difference of 1. 1, 1. 1, 1. 2 and 1. 3 cm for girls and 1. 1, 1.
Financial supportMB was financially supported by an educational grant from the Regional Health Agency of Ile-de-France. PS was financially supported by the French Ministry of Health; the Laboratoires Guigoz-General Pediatrics section of the French Society of Pediatrics-Paediatric Epidemiological Research Group research prize; and the Research commission of the French Association of Ambulatory Pediatrics. The ELFE birth cohort is a joint project between the French Institute for Demographic Studies (INED, Institut national d' etudes d emographiques) and the National Institute of Health and Medical Research (INSERM, Institut national de la sant e et de la recherche m edicale), in partnership with the French blood transfusion service (EFS, Etablissement français du sang), the France Public health (Sant e publique France), the National Institute for Statistics and Economic Studies (INSEE, Institut national de la statistique et des etudes economiques), the French Ministry of Health (DGS, Direction g en erale de la sant e), the Ministry for the Environment (DGPR, Direction g en erale de la pr evention des risques), the Ministry of Health and Social Affairs (DREES, Direction de la recherche, des etudes, de l' evaluation et des statistiques), the Ministry of Culture (DEPS, D epartement des etudes, de la prospective et des statistiques), and the National Family Allowance Fund (CNAF, Caisse nationale des allocations familiales), with the support of the Ministry of Higher Education and Research (INJEP, Institut national de la jeunesse et de l' education populaire).
Such an intact epithelium is able to exclude the vast majority of the microbiota from access to the subepithelial cells in the lamina propria  (49). Our results indicated that the 250 g/t XOS up-regulated the mRNA level of ZO-1. ZO-1 serves as a scaffold protein and anchors tight junction strand proteins (50). Yin et al. (51)  also have reported that dietary XOS markedly enhanced the mRNA level of ZO-1 in the ileum. However, further work is needed to determine if such an increased expression of ZO-1 is paralleled by a modification of the epithelial barrier function. Christensen et al. (52)  have reported that the relative abundances of beneficial microbiota have been found a highly association with gut barrier. But the data of our study did not prove such an association. Moreover, no differences in the mRNA levels of Occludin, Claudin 2, and Claudin 3 were recorded when comparisons between XOS-supplemented groups and blank control group were done, thus indicating that the effect of XOS on ZO-1 gene expression among other genes coding for tight junction protein appears rather specific.
Differential scanning calorimetry (DSC) The thermal characteristics of flours have been studied using differential scanning calorimetry (DSC 250 , TA Instruments, USA) calibrated using an empty pan. For each flour 2 ± 0. 5 mg were dispersed in distilled water to achieve the ratio of (30/70 w/w) (flour: water), in a hermetically sealed aluminum capsule as it was described by  Villanueva, Harasym, Muñoz, and Ronda (2018). The samples were then held for 5 min at 30 • C and then heated to 90 • C at a rate of 20 • C/min. The TRIOS software was used to determine the starting temperature (T 0 ), the peak temperature (T p ), and the ending temperature of the gelatinization (T f ), as well as the ΔH Gel (gelatinization enthalpy).
Mixture design The design of the mixture plan was carried out with the NemrodW software. Thirteen mixtures were obtained in the plan with 3 constituents (Table  1 ) according to a Scheffé matrix with lower ratio constraints (40% for chickpea, 10% for oat, 20% for coconut) and higher ratio constraints (60% for chickpea, 20% for oat, 40% for coconut) from dry matter. The centered cubic reduced mathematical model allows us to predict the values of the experimental responses from the iso-response curves, for water retention, color difference, and texture (hardness and cohesion). Eq. (  4 ) shows the cubic model that was fitted to each response, with b i representing the coefficients, and x i representing the values of the factors. y = (b 1 * x 1 ) + (b 2 * x 2 ) + (b 3 * x 3 ) + (b 12 * x 1 * x 2 ) + (b 13 * x 1 * x 3 ) + (b 23 * x 2 * x 3 ) + (b 123 * x 1 * x 2 * x 3 ) (4).
Statistical analysis The statistical analyses were performed using NemrodW software (NemrodW®, Marseille, France), which is a software package for designing and analyzing experimental and mixture design. All experiments were run at least three times and allowed for the determination of mean values and standard deviations. ANOVA tests were performed to compare the means as well as the correlation coefficients between the other parameters. The variances were considered to be significant at the threshold of 95% (p < 0. 05). The mixture results were then analyzed by NemrodW software with a cubic model.
Because the kidney is the main organ to metabolize citrulline into arginine, high plasma citrulline levels may reflect kidney failure  [11]. Most nutrients do not contain relevant amounts of citrulline; however, there are about 7-14 mg citrulline per g dry weight of watermelon and 1. 9 mg per g fresh weight  [12]. In order to know more about the physiological properties of citrulline we performed a structured literature research and hereby summarize the signaling pathways of citrulline and the current evidence for its clinical use. Literature research has been performed in April 2021 with the terms "citrulline" AND ("clinical trials" OR "trials") mentioned in the abstract or title. The research databases Pubmed, EMBASe, and Cochrane Library were accessed, and case reports and animal studies have been excluded.
Afterwards, doubles were erased, and the remaining literature was clustered by T. R. and J. L. M. and summarized in the following review. Important animal data that were repetitively cited in these studies retrieved above are also summarized in this review. The structured research found 389 articles, the same search on EMBASE explicitly excluding case reports or animal studies found 301 hits, and the Cochrane Library retrieved 263 articles. A total of 184 records were at least reported twice and erased. However, 153 published articles referred to rheumatological diseases where citrullinated proteins are mainly used as biological markers for disease severity. A total of 52 articles assess the effect of citrulline supplementation on sportive executive functions. These studies show small but positive effects of citrulline supplementation on high-intensity strength that are summarized within the review by  Trexler et al.
The relatedness of the equine-associated Escherichia coli strain ST1250 and its single-and double-locus variants (ST1250-SLV/DLV), obtained from horses in Europe, was studied by comparative genome analysis. A total of 54 isolates of E. coli ST1250 and ST1250-SLV/DLV from healthy and hospitalized horses across Europe (Czech Republic [n = 23], The Netherlands [n = 18], Germany [n = 9], Denmark [n = 3], and France [n = 1]) from 2008 to 2017 were subjected to whole-genome sequencing. An additional 25 draft genome assemblies of E. coli ST1250 and ST1250-SLV/DLV were obtained from the public databases. The isolates were compared for genomic features, virulence genes, clade structure, and plasmid content. The complete nucleotide sequences of eight IncHI1/ST9 plasmids and one IncHI1/ST2 plasmid were obtained using long-read sequencing by PacBio or MinION.