dataesr/scientific-paragraphs-categorization huggingface dataset:
S1 ) and Rv0237/LpqI did not show any activity using synthetic substrate (Table  S1 ) or M. bovis BCG AG. However, Rv3096, subsequently designed GlfH1, showed a glycosidic activity toward the galactan moiety of M. bovis BCG AG by releasing free galactose (Fig. S2 ). This protein was selected for further analyses. The Rv3096 gene is composed of 1140 bp encoding a 379amino acid residue protein predicted to contain a 27-amino acid signal peptide by the SignalP-5. 0 server  (15). The molecular weight of GlfH1 without the signal peptide was calculated at 40,382 Da. Sequence analysis by SSDB showed a Pfam Cellulase GH5 motif spanning residues 150 to 282 (Fig. 1A ). GlfH1 was classified in family GH5_13 in the CAZy database. Surprisingly, to this date, this family only contains glycosidases that use glucose or mannose-containing polysaccharides as substrates e.
1B ). A maximum-likelihood analysis for the same sequences confirms this observation (Fig. S4 )  (17). In the subfamily GH5_13, the crystal structure of several glycosidases has been solved and the two catalytic amino acid residues, the first residue allowing the nucleophilic attack and the second operating in the acid/base transition, have been identified  (18 -20). Of note, proteins of the GH5_13 family harbor two glutamic acid residues as catalytic amino acids in the CAZy GlfH1 hydrolyzes mycobacterial galactan database. From there, a multiple alignment by MUSCLE with the sequence of GlfH1 using these proteins makes it possible to highlight two candidates, Glu-170 and Glu-268, as acid/base and catalytic nucleophile residues, respectively (Fig. 1C ). His-242 is also conserved among these sequences.
Bioinformatics Sequences for the GH5_13 subfamily CAZy glycosidases from mycobacteria were extracted from their NCBI reference genome. For all the protein sequences used, the presence of a signal peptide was sought with the SignalP 5. 0 server  (15)  and the eventual signal peptide was removed from the sequence. Subsequently, the protein sequences were numbered without the signal peptide. The results obtained from the consultation of databases were respectively obtained with the release 230 (Feb 2019) for the NCBI (RRID:SCR_006472), release 2019_02 (13 Feb 2019) for UniProt (RRID:SCR_002380), 20 February release for RCSB PDB (RRID:SCR_012820) and February 2019 release for CAZy (RRID:SCR_012909). The Unipro UGENE v1. 32 (Feb 2019) bioinformatic software was used for data sequence management, multiple sequence alignments, and phylogenic analysis  (47).
Acknowledgments-We are indebted to the Plateforme d'Analyze des Glycoconjugués and to the  Research Federation FRABio (Univ. Lille, CNRS ,  FR 3688 ,  FRABio, Biochimie Structurale et Fonctionnelle des assemblages Biomoléculaires ) for providing the scientific and technical environment conducive to achieving this work. We thank  Anne Harduin-Lepers ,  Olivier Vidal ,  Isabelle Huvent ,  Emiko Matsunaga ,  Shin-Yi Yu ,  Bernadette Coddeville , and  Emmanuel Maes  for scientific and technical advice.
Edited by This work was supported by the  Centre National de La Recherche Scientifique (CNRS) , the  Agence Nationale de la Recherche  (project  MyCat ) Grant  ANR-15-CE18-0007-01  (to L. S. , Y. G. , and C. M. ), and the  Fondation pour la Recherche Médicale (FRM)  Grant  DEQ20150331719  (to I. H. and L. K. ). The authors declare that they have no conflicts of interest with the contents of this article.
Acknowledgements. This work received financial support from the  National Research Agency (ANR)  within the framework of the  GIGASSAT  ( ANR-12-AGRO-0001 ) and  ENVI-COPAS  ( ANR-15-CE35-0004 ) projects. Funds for openaccess publication fees were received from  IFREMER. The postdoctoral research contract of B. L. D. was co-funded by  IFREMER  and  ANR  ( GIGASSAT  project). The oysters used in this work to estimate the epidemiological parameters of Vibrio aestuarianus infection were produced by the IFRE-MER hatchery in Argenton and maintained under controlled conditions at the  IFREMER hatchery in La Tremblade  and at the IFREMER nursery in Bouin. We are very grateful to the hatchery and nursery teams for their assistance with oyster production. We wish to acknowledge  Bruno Petton  ( IFRE-MER, Lemar ) for his assistance with oyster production.
Thermal and crystalline properties of starch The thermal properties during starch gelatinization were determined using a Multi-Cell Differential Scanning Calorimeter (MC-DSC) -(TA Instruments, Lindon, USA). The starch samples were weighed and hydrated directly into the ampoules (10 g dry starch / 100 g suspension). An ampoule with deionized water was used as a reference and three runs for each sample were analysed. The MC-DSC heating program consisted of going from 20 to 120 °C at a rate of 2 °C/min. The onset temperature (To), the peak temperature (Tp), the conclusion temperature (Tc), and the enthalpy (ΔH) associated with the starch gelatinization interval were calculated with the aid of the Universal Analyzer software (TA Instruments, New Castle, USA). The crystallinity of starch samples was determined by X-ray diffraction (XRD).
Acknowledgments The authors are grateful to: -the  Région Pays de la Loire (France)  /  RFI "FOOD 4 TOMORROW"  for funding the Postdoctoral fellowship " STARCH-3D " of  BC Maniglia ; -the  São Paulo Research Foundation  ( FAPESP, Brazil)  for funding project n°  2019/05043-6 ; -the  National Council for Scientific and Technological Development (CNPq, Brazil)  for funding the productivity grant of  PED Augusto  ( 306557/2017-7 );.
The Survey Data from the Study on Global Ageing and Adult Health (SAGE) were analyzed. These data are publicly available through http://www. who. int/healthinfo/sage/en/. This survey was undertaken in China, Ghana, India, Mexico, Russia, and South Africa between 2007 and 2010. Based on the World Bank classification at the time of the survey, Ghana was the only low-income country, and China and India were lower middle-income countries although China became an upper middle-income country in 2010. The remaining countries were upper middle-income countries. Details of the survey methodology have been published elsewhere  [22]. Briefly, in order to obtain nationally representative samples, a multistage clustered sampling design method was used. The sample consisted of adults aged ≥18 years with oversampling of those aged ≥50 years.
Sarcopenia Following the criteria used in a previous publication using the same dataset  [23] , sarcopenia was defined as having low skeletal muscle mass (SMM) as reflected by lower skeletal mass index (SMI) and either a slow gait speed or a weak handgrip strength  [24]. Skeletal muscle mass (SMM) was calculated as the appendicular skeletal muscle mass (ASM) based on the equation proposed by Lee and colleagues: ASM = 0. 244*weight + 7. 8*height + 6. 6*sex -0. 098*age + race -3. 3 (where female = 0 and male = 1; race = 0 (White and Hispanic), race = 1. 9 (Black) and race = -1. 6 (Asian))  [25]. ASM was further divided by BMI based on measured weight and height to create a skeletal muscle mass index (SMI)  [26]. Low SMM was defined as the lowest quintile of the SMI based on sex-stratified values.
Discussion In our study, we found that fruit consumption is overall significantly associated with lower odds for sarcopenia among adults aged ≥65 years in LMICs, but that this association was only found among females. Specifically, compared to women in the lowest levels of fruit consumption (Q1), those in Q4 and Q5 had an approximately 60% lower odds for sarcopenia. Vegetable consumption was not associated with sarcopenia in our study. The strengths of the study include the large sample size and the use of nationally representative datasets from six LMICs which comprise nearly half of the worldwide population  [22]. To the best of our knowledge, our study is the largest study on this topic to date, while it is also the first study from LMICs. The inverse association between fruit consumption and sarcopenia observed in our study may be explained by the effects of antioxidant nutrients such as vitamin C and carotenoids  [35] , which are found in abundance in fruits  [13].
Funding: This research received no external funding. Acknowledgments: This paper uses data from  WHO's Study on Global Ageing and Adult Health (SAGE). SAGE is supported by the  U. S. National Institute on Aging through Interagency Agreements   OGHA 04034785 ,  YA1323-08-CN-0020 ,  Y1-AG-1005-01  and through research grants  R01-AG034479  and  R21-AG034263. Ai Koyanagi 's work is supported by the  PI15/00862  project, integrated into the National R + D + I and funded by the  ISCIII-General Branch Evaluation and Promotion of Health Research  and the  European Regional Development Fund (ERDF-FEDER).
Statistical Analysis The results were processed with the XLSTAT (2015) software for Windows. Each animal was considered to be the fundamental experimental unit, and the cage effect was taken into account by using a cage repetition effect in a nested model designed for ANOVA. The analysis of variance was then performed to investigate the effects of the diet (control diet with 0. 295% Trp vs. diet with 2% Trp), the effect of supplementing the drinking water with Pro, the effect of cage repetition, and the diet by Pro interaction and Y ijk 5 D i 1 P j 1 C k 1 DP ij 1 E ijl , where D i was the Diet effect, P j was the Pro effect, C k was the Cage repetition effect, and DP ij the interaction between Diet and Pro effects and E ijkl the residual. An LSD-Fisher test was used for multiple comparisons.
Optical microscopy Optical microscopy observations were performed using the IX70 inverted microscope (Olympus, Japan) in polarized mode and a DP-soft camera (Camedia digital camera, C4040 Zoom, Olympus, Japan) connected to a computer. In order to facilitate microscopic observation in polarized light, pigments and mother-of-pearl have been removed from the finished formulations. Samples were prepared by depositing a small quantity onto a glass microscope slide. The formula was pressed with a glass cover slip to ensure a sample thin enough for polarized light microscopy. The polarizer and analyzer were not in a fixed cross orientation and could be rotated. The samples were observed with a x10 objective (CPlanFI, Olympus, Japan) and a x40 objective (LCPlanFI, Olympus, Japan). Images were obtained using Cam2Com digital camera control software (Sabsik, US).
This type of experiment makes it possible to identify the behavior under flow of the samples, i. e. to know the evolution of the viscosity when the shear rate increases. For example, if the samples are shear-thinning, this means that their viscosity decreases as the shear rate increases. In addition to the viscosity evolution as a function of the shear rate, the yield stress was also determined. This is the stress that must be applied for the sample to start flowing. For the analysis of the results, we processed the data after applying the Rabinowicz correction and then the Herschel-Bulkley model directly from TRIOS ®. The Rabinowicz correction is necessary to correct overestimated results when the rheology experiments took place with a parallel plate geometry such as UHP. Indeed, for a coneplane geometry, due to the conical shape, the height of the air gap is lower at the center, therefore the shear of the sample is constant over the entire surface of the geometry.
290 Å À1 corresponding to a characteristic distance of 43 Å. For the new formula based on jojoba butters, the first two peaks are at 0. 112 Å À1 and 0. 224 Å À1 corresponding to a characteristic distance of 56 Å. Finally, for the positive control formula the first two peaks are at 0. 099 Å À1 and 0. 199 Å À1 Table  4. Sensory evaluation (texture and wear on the eyelids after 8 h) and instrumental data (rheological properties and organization at the microscopic and molecular scales) obtained for the positive control (long-lasting formula), the negative control (formula that migrates very quickly into the eyelids) and the new formula based on the mixture of jojoba esters (75/25% w/w butter A/butter B).
Genomics The first completely sequenced genome of the LAB group was L. lactis subsp. lactis IL1403 strain, published in 2001. This study revealed biosynthetic pathways, phages and some of the components that participate in aerobic metabolism  (Bolotin et al. , 2001). In 2002, a program intended for the mass sequencing of LAB genomes was announced by Lactic Acid Bacteria Genome Sequencing Consortium  (Klaenhammer et al. , 2002). Currently, more than 100 Lactococcus genomes are available on the NCBI database (National Center for Biotechnology Information http://www. ncbi. nlm. nih. gov/genome/genomes/156), of which 39 are complete genomes. LAB have small genomes, approximately 2Mb in length on average, coding for approximately 2000 genes, but range from 1600 to 3000 genes, according to the species.
They complement each other, providing greater knowledge and understanding of new and/or difficult-to-grow bacteria. A database was created in order to group several prokaryotic species associated with human beings (commensals or pathogens), highlighting the importance of culturomics and metagenomics. The 2172 species listed were classified into 12 different phyla, most of them being Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes  (Hugon et al. , 2015). More recently, it was reported that the number of species had increased, totalng 2776 species, due to culturomics techniques that facilitated the identification of new bacterial species  (Bilen et al. , 2018). Stool samples of malnourished and healthy patients from Senegal and Niger were analyzed using culturomics and metagenomics.
For example,  Bianchi et al. (2020)  identified altered amino acid production, as well as metabolic and health-promoting changes in probiotic strains of L. paracasei, Streptococcus thermophilus, and bifidobacteria as a result of different conditions of manufacture and formulation through an integrative approach of functional proteomics, metabolomics, and in vivo analyses. Although promising, integrative omics currently presents great challenges such as a need to development and employ bioinformatics pipelines and algorithms to associate and harmonize large amounts of data generated by the different high-throughput platforms  (Jiménez-Pranteda et al. , 2015). Recently, feature-annotation enrichment analysis has been extensively used to identify biological processes by comparing de novo data with accumulated biological data deposited in public databases.
Similarly, the DcadAfbpBC mutant was more sensitive to Cd 2+ than the single mutants (Fig. 4D ), confirming that fbpBC was also involved in Cd 2+ tolerance. Altogether, these data strongly indicated that the iron acquisition FbpA/FbpBC system and very likely iron uptake were required for Cu + and Cd 2+ tolerance in the absence of the efflux detoxification systems. The Ftr iron import system is also required for metal tolerance The fbpAKm and DfbpBC mutants still grew in the malate medium with excess Cu + or Cd 2+ suggesting the presence of other iron uptake systems. To analyse the R. gelatinosus response to iron limitation, the wild-type and fbpAKm strains were cultured in parallel either in iron-containing or in iron-depleted media and periplasmic fractions were analysed on SDS-PAGE. This analysis revealed a strong induction of a 19 kDa protein  (Figs 3A and 5A).
The search for periplasmic proteinencoding genes within the R. gelatinosus genome database suggested that this protein might correspond to FtrA (also annotated as P19), involved in Fe 3+ uptake. To ascertain that the induced protein under iron-limiting condition corresponded to FtrA, the ftrA gene was inactivated in the wild-type strain and the periplasmic protein content was compared under iron-rich and irondepleted condition. The analysis confirmed that the identified band corresponded to FtrA as it was absent in the DftrATp strain (Fig. 5A ). FtrA/P19 is the periplasmic iron-binding protein of the tripartite FtrABC (EfeUOB) and P19-Ftr1P system identified in Escherichia coli strain O157:H7 and Campylobacter jejuni respectively  (Cao et al. , 2007; Liu et al. , 2018). FtrA encoding gene in R.
mRNA preparation and RT-PCR Total RNA was purified from wild-type cells grown in photosynthesis condition in malate medium (M), in an iron-depleted malate medium (-Fe) or in malate medium supplemented with 1 mM of CuSO 4 or 1 mM of CdCl 2 as described in  (Steunou et al. , 2013). For semi-quantitative RT-PCR, cDNA was generated from 1 µg of total RNA with random hexamers using the Superscript IV (Invitrogen) and by following the manufacturer's protocol. PCR was done with 2 µl of cDNA with specific primers (Table  S2 ) to amplify fragments of 16S, pucA (encoding the a subunit of LH2), sodB (encoding superoxide dismutase), ftrA and fbpA genes. Amplified products were analysed on a 1. 4% agarose gel, and the bands were quantified using imageJ program. The relative amount was calculated based on the signal obtained in malate medium.
Acknowledgements We gratefully acknowledge the support of the  CNRS  and the Microbiology Department of I2BC. We are very grateful to  Prof. Dietrich H. Nies  for providing E. coli strains. We also acknowledge the  National BioResource  Project,  National Institute of Genetics, Japan. ICP-MS experiments were performed in the  MasSpecLab facility in Versailles Saint-Quentin-en-Yvelines University.
Statistical analysis Data were collected via tablets using Open Data Kit software. All statistical analyses were carried out using Stata 15 (Stata Corp, Texas, USA). Characteristics of the study population were summarized as percentages and means ±SDs or, if not normally distributed as median (IQR). Linear and logistic mixed models were used to assess differences in means and proportions at admission, with study team and health centre included as random effects. Linear and logistic mixed models were used to evaluate change from admission to discharge in mean biomarker concentrations or proportions of deficiencies, as appropriate. Study team, health centre, and child id were included as random effects. Both unadjusted and adjusted models (including sex and age) were fitted. Similarly, the effect of RUTF dose on mean biomarker concentrations and proportions of deficiencies were analysed with linear and logistic mixed models.
Results Out of the total 801 children included in the trial, 402 were randomised to the reduced RUTF dose and 399 to the standard dose. Hb was analysed for all admitted children and additional biomarkers including SF, sTfR, RBP, CRP and AGP were analysed for 714 (89%) of admitted children. At discharge, we analysed Hb for 425 (98%) of recovered children and additional biomarkers were analysed for 383 (90%) of recovered children (see Fig. 1 ). As previously detailed  [18] , non-recovered children represented a heterogeneous group of children referred to inpatient care (20%), defaulters (12%), lost to follow-up (0. 1%), deaths (0. 1%), nonresponders (13%) and false discharges (3%). Because of ethical and operational constraints, vitamin A and iron biomarker data were only obtained from 30% of these children, mostly from the nonresponders.
BDCA2 is an inhibitory receptor expressed on pDC which, once engaged, inhibits the production of type I IFN  [23]. A proof of concept study showed that a monoclonal antibody directed against BDCA2 (BIIB059) improved the cutaneous lesions of systemic lupus erythematosus (SLE), and a phase II clinical trial is ongoing in cutaneous lupus erythematosous  [24]  (NCT02847598). Another strategy to block the IFN-a pathway would involve the use of antibodies directed against the cytokine itself or its receptor, interferon alpha and beta receptor (IFNAR). The use of sifalimumab and anifrolimumab, targeting IFN-a and its receptor, respectively, has proven to be effective for the treatment of SLE  [25, 26]. These strategies could therefore be a reliable option to inhibit the initiation of the disease.
Ethics The NutriNet-Santé study is conducted according to the guidelines from the Declaration of Helsinki and was approved by the ethics committee of the French Institute for Health and Medical Research (IRB Inserm no. 0000388FWA00005831) and by the National Commission on Informatics and Liberty (CNIL no. 908450 and no. 909216). All subjects signed an electronic informed consent. This study is registered in ClinicalTrials. gov (NCT03335644).
Dietary data and Organic Food Consumption An optional organic food semi-quantitative frequency questionnaire (Org-FFQ) was proposed to the cohort participants (June -December 2014). This questionnaire is originally based on an original validated FFQ  (35)  and has been described elsewhere  (36). Participants were asked to report their frequency of consumption and portion sizes over the past year for 264 food and beverage items. The portion sizes for each food consumed were estimated according to standard measurements (e. g. , home containers, grams displayed on the package or photographs available via the interactive interface). These photographs came from a validated picture booklet  (37). The frequency of consumption referred to usual consumption over the past year on an increasing scale including yearly, monthly, weekly or daily units, as suitable.
Nutrient intakes were estimated using a published nutrient database  (38). Only participants with a plausible energy intake were included in the analyses, the over-reporters and under-reporters were excluded. They were identified by a ratio of energy intake to energy requirement, estimated with the Schofield equations according to sex, age and BMI  (39). Energy requirement, accounting for physical activity level, was compared with energy intake. The ration between energy intake and energy requirement was calculated and participants with ratios below or above cutoffs previously identified (below 0. 35 or above 1. 93) were excluded. To assess the adherence to the nutrient-based French recommendations, the probability of adequate nutrient intake (PANDiet) was computed  (40). This 100-point score represents the average of two sub-scores: the adequacy sub-score estimating the proportion of adequacy for 21 items for which the usual intake should be above a reference value, multiplied by 100, and the moderation sub-score corresponding to the proportion of adequacy for six items for which the usual intake should not exceed a reference value, multiplied by 100.
Sample selection Of the initial 121,266 participants who received the optional questionnaire on food exclusions, a total of 34,781 completed it. Within this sample, we excluded participants who reported a diagnosed CD, with missing sociodemographic data and living overseas, and those who did not completed the Org-FFQ. The final sample available for analysis included 23,468 individuals (Figure  1 ) including 499 total gluten avoiders, 2,023 partial avoiders, and 20,946 non-avoiders. The percentage of participants avoiding gluten in this study was 10. 75%, 2. 13% of whom totally excluded gluten.
Organic food consumers reported the same trends in food groups  (48)  : the most popular organic food groups were eggs in first, fruits and vegetables, whole starchy foods and oils, and the least popular were meat and dairy products. The data of this study are in accordance with ones of a recent US study about people who value gluten-free products  (25). In this study, individuals who value gluten-free products had healthy behaviors: they had a higher consumption of vegetables and fruits and a lower consumption of sugar-sweetened beverages as well as a higher intake of fiber and lower Downloaded from https://www. cambridge. org/core. INRAE -Toulouse, on 07 Oct 2020 at 14:39:06, subject to the Cambridge Core terms of use, available at https://www. cambridge. org/core/terms. https://doi. org/10.