dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements This work was supported by the  Labex   MS2T  through the program "Investments for the future" funded by the  French Government  and managed by the  National Agency for Research (Reference   ANR-11-IDEX-0004-02 ). It also received funding from the  European Research Council (ERC)  under the European Unionâ ȂŹ s  Horizon 2020 research and innovation programme  (Grant agreement No. ERC-2017-COG -MultiphysMicroCaps ).
Study Design and Plasma Samples The GABII (Globulines Anti-lymphocytaires polyclonales et Barrière Immunitaire Intestinale) cohort (NCT02843841, protocol number P/2014/221) is a prospective, longitudinal study designed to assess the effect of anti-thymocyte globulins on gut barrier and microbiota in kidney transplantation setting. Exclusion criteria were an infectious episode within the last month before transplantation, an ongoing antibiotherapy at time of inclusion, or a chronic infectious disease (hepatitis B or C viruses, or HIV). Sixty-eight consecutive patients have been enrolled (Table  1 ). Samples were collected and sent to the Biomonitoring Platform (Etablissement Francais du Sang (EFS), Besancon, France) for processing and storage. For each patient, blood samples were collected prior to transplantation (ESRD) after at least 6 hours of fast, either from fistula when hemodialysis was required before transplantation (n=17 among 43 patients on hemodialysis) or from peripheral vein (n=51, i.
Statistical Analysis All results are depicted as median with interquartile range (median [interquartile]) or mean with standard deviation (mean ± SD). The Mann-Whitney U test was used for pairwise comparison. The correlation studies were assessed with nonlinear regression (Spearman) and represented with linear regression. Differences with a p-value below 0. 05 were considered statistically significant (*p<0. 05; **p<0. 01; ***p<0. 001; ****p<0. 0001). Data were performed using GraphPad Prism 5 (GraphPad Software, San Diego, CA).
Moreover, monocytes stimulated with serum containing the highest proportion of C18 LPS were less prone to secrete high amounts of pro-inflammatory cytokines. Cytokine levels found after stimulation with C18 LPS-enriched sera from ESRD patients were found similar than those measured after monocyte stimulation with HV serum. This confirms that composition and equilibrium of circulating LPS subtypes rather than total circulating LPS quantity directly influence LPS-induced inflammation. Thereby, the pathogenicity of circulating LPS depends more on its subtype composition and on the plasma neutralization capacities than on total LPS concentrations. Biomarkers of gut bacterial integrity are difficult to interpret in the setting of ESRD. Although we also quantified plasma iFABP (intestinal fatty-acid binding protein) concentrations (Supplementary Figure  S3A ) -an intracellular protein specifically and abundantly expressed in the epithelial cells of the mucosal layer of the small and large intestine tissue  (28)  and a non-invasive biomarker for evaluating gut wall integrity lossin both groups, we chose to not include these data to our report.
FUNDING This work was supported by grants from the  Fondation Transplantation , the PHRC 2005 and 2011 (to DD), the  Fondation de France  ( Appel d'offre "Maladies Cardiovasculaires " 2007 No. 2007 001859  [to PS]), the  DHOS/INSERM/INCa  ( Appel d'offre Recherche Translationnelle 2008  [to DD and PS]), and the  APICHU 2010  and  2014  (to JB), from the  Agence Nationale de la Recherche  ( Labex LipSTIC ,  ANR-11-LABX-0021 ) and the  Reǵion de Franche-Comté (support to  Labex LipSTIC  [to PS] 2018 and 2019). JB received financial support from the  Fondation Transplantation  (No. ET-031211  and No. ET-050320 ). CC received PhD grant from the  University of Franche-Comte. HA-R received PhD grant from the  Reǵion de Franche-Comte. This work is a part of the  RIALTO (Research in Immunology of AtheroscLerosis after TransplantatiOn) program.
Microscopy and Imaging An Olympus BX50 Microscope (Model U-SD0, Olympus Optical Co. , Ltd. ) with an Olympus DP70 camera and Olympus U-CMAD3 adapter was used with the AnalySIS program for imaging. For enumeration of POU2F3 + cells, five images at x40 magnification were acquired for each tissue section, ensuring no overlap and samples scored blind. All epithelial cells were counted using Image J  (22). Following counting of all POU2F3 + cells within the epithelial cells, the percentage of POU2F3 + cells/all epithelial cells was calculated. The mean percentage of POU2F3 + cells was calculated across the five images for each sheep.
1% PBS-Tween20, PBST), and probed overnight at 4°C with primary antibody: anti-POU2F3, 1:2500 (Sigma-Aldrich, HPA019652) or antiactin, 1:1000 (Sigma, A-3853) before incubation for 1 hour at RT with secondary antibody: anti-mouse peroxidase, 1:20,000 (Sigma, A-2304) or anti-rabbit peroxidase, 1:10,000 (Sigma, A-0545). Following washing in PBST, membranes were re-joined and signal developed using SuperSignalTM West Pico PLUS Chemiluminescent Substrate (Thermo Scientific) and captured on x-ray film.
Tuft Cell Sub-Cluster Trajectory Inference and Pseudotime Analysis To further analyze ovine tuft cells, we repeated the clustering step on these cells (PCA dimension of 15 and cluster resolution of 0. 5). For trajectory inference, tuft cells were plotted using PHATE maps (27) (using the same genes as for PCA) and trajectories identified using slingshot  (28) , with sub-cluster 1 defined as the putative starting point. Genes with expression patterns associated with progression of the trajectory were identified using generalized additive models with tradeSeq package v1. 3. 18104 default parameters. Differential expression analysis was carried out using tradeSeq association Test function with default parameters, and significant genes (log FC > 0. 25) clustered using tradeSeq clusterExpressionPattern.
Identification of Ovine Abomasal Tuft Cells by Immunohistochemistry To determine if cells characteristic of tuft cells are present in the ovine abomasal epithelium, antibodies to human POU2F3, GFI1b, TRPM5 and DCLK-1 (15) (Supplementary Table  2 ) were tested by immunohistochemistry (IHC). Analysis of ovine genome data (https://www. ensembl. org/Ovis_aries/Info/ Annotation) identified sufficient conservation (Supplementary Table  3 ) to suggest antibody cross-reactivity. We first examined samples at 21 days post-infection (p. i. ) with T. circumcincta, a time-point at which adult parasites are present in the abomasum lumen. Clear labelling of POU2F3 + epithelial cells, consistent with the distribution of tuft cells in mice, was observed (Figure  1A ). Western blot of transfected HEK cells expressing ovine POU2F3 confirmed specificity of the anti-POU2F3 antibody (Supplementary Figure  1 ).
scRNA-Seq Identifies Distinct Ovine Epithelium and Immune Cell Types Detailed analysis and clustering of scRNA-seq data was carried out using R toolkit Seurat 3. 0 (http://satijalab. org/seurat/) (25). Ovine and bovine mapped data identified similar numbers of cell clusters; due to the higher number of mapped reads and better annotation, we focused on the bovine data. Datasets from the two samples were integrated using the canonical correlation analysis (CCA) method (  26 ) and hierarchical clustering generated 15 distinct groups, (see Figure  3A ). Based on POU2F3 expression, a tuft cell cluster was identified and all clusters were annotated as far as possible (Figure  3A ) based on expression of marker genes identified here (Supplementary Table  5 ) and in previous studies of epithelial  (31) , tuft (9, 32) and immune cell genes.
FUNDING KH is supported by an  Industrial Partnership PhD studentship  funded by  University of Glasgow ,  Moredun Foundation  and  Pentlands Science Park, UK. TM is supported by the  Scottish Government's Rural Affairs, Food and the Environment (RAFE)   Strategic Research Portfolio 2016-2021. VG and SL are funded by a  Wellcome Trust   Collaborative Award  ( Ref 211814 ) to CB, ED, TM, PJ, and RM; SL and RM also received  Wellcome Trust  support through an  Investigator Grant  ( Ref 219530 ), and the  Wellcome Trust  core-funded  Wellcome Centre for Integrative Parasitology  ( Ref 104111 ). TDO is supported by  Wellcome Trust  grant  104111/Z/14/ZR.
DATA AVAILABILITY STATEMENT The datasets presented in this study can be found in Supplementary Material or in online repositories. scRNA-seq data are available in the ArrayExpress database at EMBL-EBI (www. ebi. ac. uk/arrayexpress), accession number E-MTAB-10231. Scripts for scRNA-seq analysis are available on request. A searchable cell atlas of scRNA-seq cluster expression data can be queried at: http://cellatlas. mvls. gla. ac. uk/Ovine_Abomasum.
Data sources and search enquiries In aim of answering the research question, a PubMed search of the literature was conducted, with the following Medical Subject Headings (MeSH): DHA, EPA, omega-3, PUFAs, with their effects on brain structure, morphology, and volume. Citations in the retrieved articles were also manually reviewed to identify studies that might have been overlooked in the database searches. Inclusion criteria were: papers published in English, investigating changes in brain structure and volume according to omega-3 fatty acids levels, using neuroimaging techniques. Accepted means of measurements of omega-3 levels included both RBC (Red Blood Cell) and plasma omega-3 testing, as well as dietary questionnaires assessing for marine product intake. Supplementation trials (omega-3 supplementation) that aimed to study the same outcome were also included in the search.
, 2012). It was also seen that participants in the lowest quartile for RBC DHA had smaller total brain volumes and greater white matter hyperintensities. Titova et al. (2013)  tested whether cognitively healthy older individuals with a higher dietary intake of EPA and DHA would have higher cognitive test scores and a greater brain volume compared to cognitively healthy older individuals with lower intakes. Their data included 252 individuals from the Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) cohort. The dietary intake of EPA and DHA was assessed by a 7-day food protocol at age 70 years. At age 75, global cognitive function was examined, and their brain volumes were measured by MRI  (Titova et al. 2013 ). It was observed that higher self-reported dietary intake of EPA and DHA was positively associated with global grey matter volume, as well as with increased cognitive performance score.
0-4. 3 cm 3 ) increase in total brain volume. With respect to the brain regions in which positive effects were observed, from white matter regions, the corpus callosum had the largest increase in volume in response the increase in omega-3 index, while the hippocampus had the largest rise from the grey matter regions. Raji et al. (2014)  studied a population of 260 cognitively healthy, un-institutionalized individuals aged 65 years and above, participants of the Cardiovascular Health Cognition Study, from whom dietary fish consumption was studied between 1989 and 1990, and MRIs were performed between 1998 and 1999. Data revealed that weekly consumption of baked or boiled fish was positively associated with grey matter volumes in the hippocampus, precuneus, posterior cingulate, and orbital frontal cortex.
65 gm dose of triacylglycerol form EPA and DHA) can safely slow the progression of white matter lesions (primary endpoint), total brain and medial temporal lobe volume atrophy and increase cerebral perfusion (secondary endpoints) in older non-demented adults with MRI and plasma evidence of white matter burden and suboptimum plasma omega 3 at baseline (clinicatrials. gov: NCT01953705). In addition, both DHA and EPA helped in reducing blood pressure, inflammation and triglyceride levels, lowering the risk of thrombotic effects and rates of cerebral atherosclerosis  [2, 24, 48, 49, and 50]. In AD, on the other hand, the proposed mechanisms for these protective effects may be related to its degenerative pathways, such that DHA and EPA help by reducing the rate at which amyloid is produced, by reducing the inflammatory cycles and the oxidative stress that result in synaptic damage, promoting higher levels of brain-derived neurotrophic factors, and by reducing arachidonic acid (omega-6) levels that pose toxicity risks at high levels  (Samieri et al.
Limitations The studies included in this review have limitations: some studies took into account dietary measurements of omega-3 intake instead of an objective measurement using, for example, blood erythrocyte omega-3 levels; most investigations were cross-sectional, and the sole RCT included was a short-term intervention; a large portion of the studies did not examine the possible confounding or mediating role of other important factors, such as other nutrients with interactive metabolism (e. g. , B vitamins) and genetics (e. g. , APOE4). Moreover, this is a narrative review that searched relevant articles in only one database; although, to the best of our knowledge, we fairly covered the available evidence, it is not excluded that potentially important articles to the topic have not been retrieved.
155 The relationships between pH, salinity, concentrations of ammonium and soluble reactive 156 phosphorus on the one hand, and abundances of Escherichia coli and fecal streptococci on the other 157 hand, were studied using multivariate analysis. All data (x) were log (x + 1) transformed and a 158 centered Principal Component Analysis (PCA) was performed using SigmaPlot 10 software to identify   205.
General methodology We conducted a cross-sectional observational study in primary care paediatric private practices throughout France from January 2016 to December 2017, named the CARMA study. The signed consent from at least one parent was obtained before inclusion. The study protocol was approved by local ethics and administrative authorities (CPP IDF III no. 3295) and was registered (ClinicalTrials. gov identifier: NCT02484274). We used the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines to report this study (Supplemental Table  1 ).
Data collection The study phases are described in detail in Supplemental Methods. In summary, current sociodemographic data, past and current main dietary habits and medical data were collected by the investigator at inclusion. During the month after inclusion, a dietary survey was performed according to the EFSA reference methodology. Parents recorded all ingesta per 24-hr period over three non-consecutive days (two during the week and one during the weekend) by using paper diaries, as in previous studies  [26]. Investigators and on-line research assistants helped parents complete the survey when needed. Dietary data from these diaries were double-entered, tested for consistency, and transformed by using the ANSES-Ciqual nutrient composition table for non-infant foods  [27]  and the infant-specific table designed for the French Children's Food Union  [28].
Main results With a simultaneous collection of medical, biological and dietary data at the national scale, a design rarely achieved in the literature  [23, 24] , we found a protective role of YCF use on ID in children at age two years in the general population. This protective role was strong with, for example, a reduction of one-fifth of ID with YCF use after age 10 months (OR 0. 15, 95% CI 0. 07e0. 31). This protective role was consistent according to the different definitions of YCF consumption (amount, duration), measured either retrospectively by asking parents about the past consumption or prospectively by quantifying current consumption with a dietary survey. This protective role is consistent with results from clinical trials [11e17] and previous observational studies [23e25,33] and was independent of potential confounders such as disadvantaged social situation, non-dairy iron intake and iron supplementation, which were not always taken into account in previous studies  [23, 24].
Strengths and limitations Our study has several strengths. The measurements of iron biomarkers were standardized and centralized as recommended by the World Health Organization  [47] , as was the evaluation of nutritional intake with a dietary survey performed on three non-consecutive days to improve the accuracy of intra-individual variability, as recommended by the EFSA  [26]. Biological and dietary data were measured independently, with blinding. A specific strength of this study is the consideration of all sources of iron besides YCF in multivariate analyses in contrast to some other national studies  [23, 24]. There were several limitations. First, the analyzed population presented a selection bias as shown by less frequent disadvantaged situations than in all births. This bias can be explained mainly by recruitment by pediatricians and the significant attrition due notably to failure to obtain a blood sample (32% of the studied population).
Treatment. The ultimate challenge in AD is to treat causally. Mirroring WD, a Zn-based therapy could be used to correct the Cu imbalance: a proof-of-concept phase II clinical in MCI trial using non-Cp Cu > than 1. 6 µmol/L as an inclusion criterion for eligibility is started in April 2021 (ZINCAiD, EudraCT 2019-000604-15, funded by the Alzheimer's Association). An additional benefit associated with the administration of Zn is that the metal is a powerful driver for neurotrophic signaling and neuronal plasticity as it promoted the maturation of the Brain-Derived Neurotrophic Factor (BDNF) from pro-BDNF through the activation of Zn-dependent Matrix metallopeptidases  [83, 84]. It has also become clear that in it is important to leave the Zn in place and hence in chelation therapy targeting weakly and Aβ-bound Cu, selective Cu chelators are required  [85, 86].
ACKNOWLEDGMENTS The  Italian Ministry of Health  funded this study (Ricerca Corrente; RS). The study is also funded by the  Alzheimer's Association Part the Cloud: Translational Research Funding for Alzheimer's Disease (PTC)   PTC-19-602325  (RS, SLS). The authors thank  Ilaria Simonelli  and for figure preparation. AG is supported by the  European Union 's  Horizon 2020 Research and Innovation Program  under the  Marie Skłodowska-Curie  grant agreement iMIND-No. 841665.
After purification on AMPure beads (Beckman Coulter Inc. , Fullerton, CA, USA), the first library was pooled with 95 multiplexed samples and the second library with 41 multiplexed samples. The global concentration was quantified by a Qubit assay with the high sensitivity kit (Life technologies, Carlsbad, CA, USA). Before loading for sequencing on MiSeq (Illumina Inc, San Diego, CA, USA) the pool was diluted at 8pM. Automated cluster generation and paired-end sequencing with dual index reads was performed in a single 39-hour run in a 2x250bp. The paired reads were filtered according to the read qualities. The raw data were configured in fastq files for R1 and R2 reads. Operational taxonomy units (OTUs) and taxonomic assignment were performed as reported previously  [25].
Statistics Statistical analyses were performed using SPSS software version 20. 0 (IBM, Paris, France), SAS 9. 4 statistical software (SAS Institute, Cary, NC) and GraphPad Prism 9. 0 (GraphPad software, La Jolla, USA). To test for a statistical association between the detection of L. monocytogenes and severe acute malnutrition using qPCR and/or culture, we used the bilateral Barnard exact test  [26]. Quantitative data distribution was assessed using the Kolmogorov-Smirnov and Shapiro-Wilk normality tests. Quantitative variables were compared using the bilateral Student test or Mann-Whitney test depending on the data distribution assessed by the normality test. All tests were two-tailed with a significance threshold set at a value of p� 0. 05.
Phylogenetic conservation of Listeria monocytogenes across anatomical niches and countries in West Africa As L. monocytogenes had an increased prevalence in several African datasets  [18, 19]  and to clarify whether a hyperendemic clone was circulating in Africa, we analysed the pangenome of the eight strains previously isolated from human milk in Mali  [18] , the 10 strains isolated in this study, and the strain isolated from a vaginal sample from a woman in Senegal who had miscarried. The orthoANI analysis of the eight genomes of the strains isolated from the milk  Senegal (Q1049), and an isolated strain from a clinical sample (blood) in France in our laboratory (P9990) with the reference genome of the type strain of L. monocytogenes, orthoANI values ranged from 98. 53 to 100% with all the African strains clearly clustered with orthoANI values ranging from 99.
Traditionally, the first 3 of these endpoints have relied on subjective as opposed to objective data and therefore may have been overstated somewhat as investigator-reported events  (27). Pre-existing rates of diabetes at or before randomization, however, were underreported by site investigators. This underidentification was striking, and it explains why approximately one-third of cases were negatively adjudicated by the CEC. Furthermore, this discrepancy illustrates that diabetes is often systematically undetected in patients and requires the careful due diligence of cardiologists and primary care physicians for accurate diagnosis, especially in patients at high risk for cardiac events. STUDY LIMITATIONS. Data on CV death were taken solely from the CEC-adjudicated group, because investigators were not required to distinguish between CV and non-CV death at the time of endpoint assessment, thereby not allowing assessment of concordance rates for this endpoint.
) for all patients were reviewed by CEC cardiologists for silent MIs. Silent MIs were identified based on the presence of new Q waves on a patient's ECG. An endpoint management team compiled and electronically provided event packets to the CEC via an adjudication database. Two primary adjudicators were assigned to each potential endpoint. If the primary adjudicators could not reach consensus, the CEC chair provided final adjudication. Additional specifics regarding the design of REDUCE-IT have previously been published (18). CLINICAL ENDPOINTS. The primary endpoint was a composite of CV death, nonfatal MI (including silent MI), nonfatal stroke, coronary revascularization, or unstable angina requiring hospitalization. The key secondary endpoint was a composite of CV death, nonfatal MI, and nonfatal stroke.
[67]  and the related database "Human Protein Atlas" available online: http://www. proteinatlas. org accessed on June 2021). Adapted from "Detection of PAMPs by Toll-Like Receptors (TLRs) and Innate Immune System: Cellular Locations of Pattern Recognition Receptors "templates (Biorender). Retrieved from https://app. biorender. com/biorender-templates, accessed on 23 September 2021). For more information see refs. [59, 63, [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84].
Acknowledgements. We thank all colleagues from the  CarMeN laboratory, CRNH Rhône-Alpes  and partners who have contributed and/or who are co-authors of our publications cited in this review, and particularly  Laure Gabert  and  Valérie Sauvinet  ( CRNH-Rhône Alpes ),  Fabienne Laugerette ,  Armelle Penhoat ,  Pascale Plaisancié ,  Manon Lecomte ,  Marine Milard ,  Bérengère Benoît ,  Chloé Robert  ( CarMeN laboratory ),  Carole Vaysse ,  Florent Joffre  and  Leslie Couëdelo  (ITERG), and  Claire Bourlieu-Lacanal (INRAE). Mélanie Le Barz  thanks the  Société Francophone du Diabète  for its postdoctoral fellowship in partnership with  AstraZeneca. Marie-Caroline Michalski  thanks for fundings the  Carnot LISA Institute , the  Francophone Diabetes Society , the  Francophone Nutrition Society  and the  CNIEL.