dataesr/scientific-paragraphs-categorization huggingface dataset:
This study used Dielmo as the control village and Ndiop as the test village. In the control village, no intervention was undertaken. Preparatory meetings with the inhabitants of the two villages were organised. The populations were informed and made aware of the objectives of the study and the importance of respecting the instructions. In particular, the inhabitants of the control village were invited to maintain their health and social habits. On the other hand, for the test village, the population was invited to use soap every day for washing hands and the body. This study was divided into five parts that were intended to allow capture of social, clinical and health events, bacteriological diagnoses and soap use during the study period. Social data and biological samples were obtained through a quarterly survey questionnaire followed by skin swabs taken from the palms of the hands.
Participants and procedures From January to December 2016, the study was conducted in the villages of Dielmo and Ndiop. The aim was to study the impact of the daily use of an unscented soap (Marseille-type soap) on fevers and respiratory and diarrhoeal diseases. Data were collected through daily active and passive monitoring in both villages during the study period. The study design is summarised in Figure  1 , including different stages of the study, with details of the numbers of children aged <5 and <15 years. Participants. Residents of all ages and of both sexes from both villages were targeted to participate in the study. In Ndiop, the participants had to commit to complying with the soap use instructions. They also had to agree to use only the soap given to them by the project. In Dielmo, the participants had to commit to not changing their lifestyle or being influenced by the distribution of soap in Ndiop.
Clinical surveys. From January to December 2016, the field workers (two per village) met daily with each participant to record their temperature and check their health. Whenever the sought symptoms were detected, the patient was referred to the village health post for a consultation with the nurses. Data on the participant's health status were recorded on the registration documents kept by the investigators, and data from the consultations were recorded on pathological episode forms. Soap distribution. In each village, concessions were divided into households headed by a wife. Ordinary solid Marseille soap type, based on sodium hydroxide, was used. The soap was not supplemented with a specific antibacterial agent. During the 6FAM-GGG ATA GAG CAG GAG GTG TCT GTC TGG-TAMRA distribution of soap in the test village, concession chiefs, wives and older children received soap for their personal use, while smaller children were organised into groups of three individuals who shared the same soap.
The strains used as positive controls are available on the Rickettsia Unit Strains Collection (CSUR, WDCM 875) under the following accession numbers: S. pneumoniae CSURP5700, S. aureus CSURP2200 and S. pyogenes CSURP6897  (Ndiaye et al. , 2018). For each species, approximately ten colonies were suspended in 200 mL PBS, and DNA was extracted  (Ndiaye et al. , 2018). The primers and probes used for pathogenic identification are listed in Table  1. The quality of the DNA handling and the extraction of the swab suspensions was verified by quantitative PCR for a housekeeping gene coding for βactin, as previously described  (Ndiaye et al. , 2018; Mediannikov et al. , 2010). Samples were considered to be positive if both specific qPCR reactions were positive using a cycle number at the threshold level for a log-based fluorescence (Ct) value <35.
Acknowledgements We would like to thank the  Mediterranean Infection Foundation  and the  French National Research Agency  through the  Investissement D'avenir program  (Grant Number  ANR-10-IAHU-03 ), which funded this study. We also would like to thank the technical staff of the  Dielmo and Ndiop  project for their contribution to the data and sample collection, and the people of both villages for their participation and collaboration in this study.
The X-ray fluorescence signal was detected with two custom energy dispersive detectors (Rayspec Ltd) at either side of the sample, holding a total of ten silicon drift diodes. The quantitative data treatment of the SXRF data was performed with Python scripts exploiting the PyMCA library  (Solé et al. , 2007) , using the fundamental parameter method with the equivalent detector surface determined by calibration with a thin film reference sample (AXO DRESDEN GmbH). The resulting elemental areal mass density maps (units: ng. mm -2 ) were visualized with ImageJ. The X-ray phase contrast imaging (PCI) exploits in-line holography. It is performed on the same instrument moving the sample a few millimeters downstream of the focus and recording X-ray in-line holograms with a FReLoN CCD based detector located 1.
Statistical analysis For nano-SXRF data analysis of element distrbutions, Pearson correlation coefficients were calculated using R software (R Core Team, 2019) with rcmdr package  (Fox & Bouchet-Valat, 2019). For fluorescence microscopy experiments, fluorescence intensity was normalized against the median of the control group for each experiment. Normality of distribution and homogeneity of variances were respectively checked with Shapiro-Wilk test and Bartlett's test. Comparison of normalized intensity between two independent groups was performed using t-test or Mann-Whitney test if normal distribution or homogeneity of variance were not met. ANOVA was used for comparison of three groups, with Tukey post-hoc test for pairwise comparisons. Kruskal-Wallis test was run when assumptions of normality or homogeneity of variances were not met.
Significant Kruskal-Wallis test (p<0. 01) was followed by Dunn's test with p-values adjusted for pairwise comparisons (Holm's method). Statistical analysis was made using Rstudio v 1. 2. 5001 (RStudio Team, 2015), R software v3. 6. 1 (R Core Team, 2019) with rcmdr  (Fox & Bouchet-Valat, 2019) , tidyverse  (Wickham et al. , 2019) , ggpubr (https://rpkgs. datanovia. com/ggpubr/), rstatix (https://rpkgs. datanovia. com/rstatix/) packages. For details see Table  S2.
Acknowledgments This project was supported by a  doctoral fellowship  from the  University of Bordeaux  (F. D. ), a grant from  Centre National de la Recherche Scientifique (CNRS)  through the  MITI interdisciplinary program  (R. O. ), a  PEPS grant  from  CNRS  and  IDEX Bordeaux  (R. O. and D. C. ),  ERC  grant  ADOS (339541 ) and DynSynMem (787340) to D. C. and support from the  Regional Council Nouvelle Aquitaine. SXRF experiments were peformed at the  European Synchrotron Radiation Facility (ESRF), Grenoble, France. We are grateful to  ESRF  staff for assistance in using ID16A beamline. STXM experiments were performed at SOLEIL synchrotron, Gif-sur-Yvette, France. We acknowledge SOLEIL for provision of synchrotron radiation facilities and we would like to thank  HERMES  staff and  F. Porcaro  from  CENBG , for their help during the experiments.
The resulting PCR products were purified and loaded onto the Illumina MiSeq cartridge according to the manufacturer's instructions. The quality of the run was checked internally using PhiX, and then each paired-end sequence was assigned to its sample with the help of the previously integrated index. Each paired-end sequence was assembled using Flash  [38] , using at least a 10 bp overlap between the forward and reverse sequences, allowing 10% mismatch. The lack of contamination was checked with a negative control during the PCR (water as template). The quality of the stitching procedure was controlled using 4 bacterial samples that ran routinely in the sequencing facility in parallel with the current samples. Raw sequences can be found at https://data. inrae. fr/dataset. xhtml?persistentId=doi: 10.
15454/Y2AHF7. Raw sequences were analyzed using the bioinformatic pipeline FROGS  [39] , based on several R software [40] packages. Briefly, quality control and trimming was performed using Cutadapt (version 1. 18)  [41]  and Flash (version 1. 2. 11)  [38]  to keep sequences between 380 and 500 bp, sequences with ambiguous bases and sequences that do not contain good primers. Clustering was then performed using Swarm v2. 1. 2 [42]  with an aggregation maximal distance of 3 bases. Chimera were removed using VSEARCH (v2. 9. 1)  [43]  with cross-sample validation. PhiX contamination was removed using VSEARCH. Affiliation was performed using the Silva 123 16S database  [44]  and NCBI Blastn++  [45]. A phylogenetic tree was constructed using FastTree (v2. 1. 10) [46]  and sample depth was normalized using GMPR  [47].
The phylosseq package  [48]  was used for biostatistical process. Alpha-diversity was estimated using two metrics: the number of observed species (richness index) and the Shannon index. A two-way ANOVA test was then performed on these two indexes to assess maternal and weaning diet effects and their interaction. Cage effect was not considered in the statistical analysis. Beta-diversity was evaluated by calculating the weighted Unifrac distance between samples. Ordination using principal coordinates analyses (PCoA) was performed to represent samples on a 2D plot. Multivariate ANOVA was performed using adonis function (Vegan Package, https://cran. r-project. org, https://github. com/vegandevs/vegan) with 9999 permutations. Relative abundances of the major phyla and of families were compared using two-way ANOVA to test maternal, dietary and their interaction effects.
Adipose Tissue Histology Epididymal fat pads were fixed in 4% paraformaldehyde (PAF), processed and embedded in paraffin using a tissue processor (Excelsior ES; ThermoFischer Scientific, Waltham, MA, USA) for histology. Sections of 5 µm thickness were deparaffined and stained with hematoxylin and eosin for morphometric analysis, and then scanned with the NanoZoomer 2. 0 RS (Hamamatsu, Tokyo, Japan). Images were captured at 20× magnification for analysis. Five representative pictures of each section were selected for counting. A semi-automated custom image analysis protocol was developed using ImageJ software to quantify the area of individual adipocytes. Histological images were segmented, creating a binary mask and converting the image to 1-bit configuration. The adipocytes were counted if they met the following criteria: (1) the adipocyte has an equivalent sphere surface diameter between 20 and 200 µm; (2) the adipocyte has a shape factor of 0.
5-1 (circularity indicator) and (3) the adipocyte does not border the image frame. Over 10% of the adipocytes were included manually. Each adipocyte was subsequently labeled with a number to visualize the adipocytes more clearly and provide traceability for their respective quantified area. About 100 adipocytes were counted per picture. Morphometric data were then exported, and expressed as adipocyte frequency per mean diameter for statistical analysis.
Statistical Analysis Data are presented as box and whisker plots with means and min-max. At each age (3 and 6 months), the data (body weight, adiposity, gut function, qPCR data) were analyzed by two-way ANOVA testing of the maternal diet, weaning diet and maternal × weaning diet effects using the GraphPad Prism software. For adipocyte distribution analysis, Gaussian curves were fit to each dataset and a comparison of fits was performed. At weaning (dams' and pupss tissue fatty acid composition), data were analyzed by Mann-Whitney tests. Microbiota data were analyzed as described in the corresponding session. Spearman rank correlation between data was performed using cor function in R and the corrplot R package of R.
Several reports have suggested that n-6 PUFA can impact intestinal production and secretion of IAP  [28, 30, 52, 53]. IAP activity in the colon was lower in rats born to LA mothers compared to those born to C-mothers, irrespective of their weaning diet (maternal diet p = 0. 02, Figure  1D ). Finally, we evaluated local and systemic inflammation. Colonic tnf-α mRNA levels tended to be greater in rats born to LA dams compared to those born to C ones (maternal diet p = 0. 08, Figure  1E ); il-1β and mcp-1 mRNA levels were not affected by the maternal or the weaning diet (data not shown). The plasma IL-1β concentration was greater in rats born to LA mothers compared to those born to C ones, irrespective of their weaning diet (maternal diet p = 0. 004, Figure  1F ). Nutrients 2019, 11, x FOR PEER REVIEW 6 of 25.
Several reports have suggested that n-6 PUFA can impact intestinal production and secretion of IAP  [28, 30, 52, 53]. IAP activity in the colon was lower in rats born to LA mothers compared to those born to C-mothers, irrespective of their weaning diet (maternal diet p = 0. 02, Figure  1D ). Finally, we evaluated local and systemic inflammation. Colonic tnf-α mRNA levels tended to be greater in rats born to LA dams compared to those born to C ones (maternal diet p = 0. 08, Figure  1E ); il-1β and mcp-1 mRNA levels were not affected by the maternal or the weaning diet (data not shown). The plasma IL-1β concentration was greater in rats born to LA mothers compared to those born to C ones, irrespective of their weaning diet (maternal diet p = 0. 004, Figure  1F ).
Acknowledgments: We thank  Alain Fautrel  and  Roselyne Veil  from Biosit histopathology platform/core ( H2P2 ,  Université Rennes 1 ) for histochemistry process and analysis. We thank  Françoise Boissel ,  Nathalie Boulier-Monthéan  and  Daniel Catheline  for their help in animal care and lipid analysis.
Data were obtained in full-scan mode with a mass range of m/z 50-550 AMU. trans-FAME were analyzed with an Agilent 7890N gas chromatograph (Agilent Technologies) equipped with a bonded fused silica capillary column with higher polarity (BPX-90; 100 m × 0. 25 mm, 0. 25 μm thickness; SGE Analytical Science). The temperature program started at 120 °C (for 120 min in the case of trans-C16:1 analysis; for 240 min in the case of trans-C18:1 analysis), then increased to 260 °C at 10 °C/min and held for 10 min. Helium was used as carrier gas at a constant flow rate of 0. 8 ml/min. The split ratio was settled at 5:1, and samples were injected with an automatic injector (Agilent Technologies). The injection volume of the trans-FAME solution (see Section 2. 2. ) was either 0. 1 µl for trans-C16:1 analysis, or 0.
5 µl for trans-C18:1 analysis. Mass spectra were recorded with an Agilent 5975C MSD (Agilent Technologies). The mass spectrometer was operated under electron impact ionization conditions (electron energy 70 eV, source temperature 230 °C). Data were obtained in full-scan mode with a mass range of m/z 50-550 AMU. Identification of positional isomers of both trans-C16:1 and trans-C18:1 relied on (1) pure standards (Matreya, PA, USA) and (2) trans-C16:1 mix kindly provided by Pierluigi Delmonte (FDA, MD, USA), by comparison of retention times. In addition to the retention time, we also used the mass spectra of peaks to verify the correspondence with either a C16:1 fatty acid (i. e. , molecular ion M + = 268 AMU) or a C18:1 fatty acid (i. e. , molecular ion M + = 296 AMU). Peak integration was performed with MassHunter Workstation Software Qualitative Analysis Version B.
Acknowledgements EG acknowledges a  CIFRE (Industrial Agreement of Training through Research) PhD fellowship  from both the  French Dairy Interbranch Organization (CNIEL)  and the  National Association for Research and Technology (ANRT)  (CIFRE fellowship number 2015/ 1195 ). We acknowledge  AAK (Malmö, Sweden ) for providing the vegetable blends samples. We also thank  Bente Kirkhus  ( NOFIMA, Tromsø, Norway ) for providing the PHFO sample. We are deeply grateful to  Pierluigi Delmonte  ( FDA, Silver Spring, MD, USA ) for providing mixes of trans-C16:1 and trans-C18:1 isomers that allowed peak identification.
The image current is detected as a function of time and is recorded as a composite sum of sinusoidal waves with different frequencies, referred to as a transient. A Fourier transform is applied to this signal to convert it to the m/z domain and produce a mass spectrum. Consequently, detailed compositional profiles, with many thousands of unique molecular (empiric formula) assignments, can be obtained from a single mass spectrum. Dedicated data mining procedures have to be used to extract metal speciation-related data from global datasets. Furthermore, multistage fragmentation and the analysis of the dissociation patterns offer data enabling the structural characterization of element species and their unequivocal identification  (Dernovics and Lobinski, 2008a). The emerging paradigm in speciation analysis is therefore based on the assumptions that (i) large numbers of species of metal/metalloids can be ionized in parallel with all the other organic matrix constituents; (ii) all the ions can be ultimately separated in a mass spectrometer; (iii) the molecular masses can be measured with accuracy allowing the unambiguous determination of the empiric formula; (iv) information on element-species of interest can be extracted from large data sets, and (v) these metal species can be structurally characterized by multistage fragmentation and unambiguously identified.
Selenium/Sulfur Homology A particularity of selenium speciation studies is the fact that selenium shares similar chemical properties with those of sulfur and competes with sulfur in biological processes. As a rule, a selenium species is likely to be accompanied by its sulfur analog which offers multiple opportunities for the analysis of highresolution high-accuracy MS data sets. As the sulfur metabolic pathways in yeast are known  (Mapelli et al. , 2012) , lists of putative selenium metabolites for targeted analysis can be made. The accurate mass difference measurement allows the identification of the S-Se homologs in data sets. Also, as demonstrated elsewhere  (Casiot et al. , 1999)  the easier availability of sulfur standards allows the validation of the identification of their selenium analogs.
Clinical and Laboratory Measurements Patient data forms were completed by trained clinical research associates with information from patient interviews and medical records. We collected detailed medical history, including cardiovascular comorbidities and risk factors. Patients were classified with diabetes if mentioned in medical records, if they used glucose-lowering medication, or if they had HbA1c $7%. They were classified with dyslipidemia if stated in medical records or if they used lipid-lowering medications. Information on medication use, including antihypertensive agents, was obtained from drug prescriptions for the 3 months before the baseline interview. Height and weight were measured by nephrologists (or outpatient nurses) during a routine visit at study inclusion, and body mass index (BMI) was calculated.
Statistical Analyses Categorical variables are presented as percentages, and continuous variables as means AE SDs or medians (IQR), depending on the normality of their distribution, assessed graphically with QQ-plots. The percentage of missing data was less than 5% for most variables, except for the second BP reading (51. 6%). In the main analysis, we used a single BP reading as outcome and performed multiple imputation for study covariates. Analyses through the complete datasets were combined according to Rubin and Schenker's rules. 40 Median (IQR) spot uNa/K, uK/Cr, and uNa/Cr ratios were described according to age, sex, eGFR, and BMI and compared with the Mann-Whitney test. Crude and adjusted associations of BP indices, with each of the 3 ratios modeled by 4-knot restricted cubic splines, were assessed with linear models with a random intercept for each nephrology clinic.
To address the concern about the reliability of a single BP reading, we then performed 2 other sensitivity analyses: one using the mean of 2 values in the subsample of 803 patients with 2 BP readings (complete case analysis), and another in all 1660 patients with imputed second readings as needed. Multiple imputation of 100 datasets were made with the fully conditional specification method. 42, 43 Covariates included in the imputation model for BP are shown in Supplementary Table  S1 , according to whether 1 or 2 BP readings were available. The fraction of missing information was 0. 21 and 0. 45 for the second systolic and diastolic BP values, respectively. Two-sided significance tests were used, and P values <0. 05 were considered significant. All statistical analyses were performed with SAS 9.
ACKNOWLEDGMENTS We acknowledge the  CKD-REIN study coordination  staff for their efforts in setting up the CKD-REIN cohort:  Elodie Speyer ,  Sophie Renault ,  Reine Ketchemin , and all the clinical research associates. We thank  Jo Ann Cahn  for editing the English version. The  French Institute of Health and Medical Research (Inserm)   Institutional Review Board  ( IRB00003888 ) approved the study protocol, and all participants signed informed consents. The  CKD-REIN study  is funded by the  Agence Nationale de la Recherche  through the  2010 «Cohortes-Investissements d'Avenir » program  ( ANR ) and by the 2010 national  Programme Hospitalier de Recherche Clinique. CKD-REIN  is also supported through a public-private partnership with  Amgen, Fresenius Medical Care , and  GlaxoSmithKline  (GSK) since 2012; Lilly France since 2013; Otsuka Pharmaceutical since 2015; Baxter and  Merck Sharp & Dohme-Chibret  ( MSD France ) from 2012 to 2017;  Sanofi-Genzyme  from  2012  to 2015; and  Vifor Fresenius  and  AstraZeneca , since 2018.
Statistical analysis Participant characteristics, including age, gender, BMI, education level, and circulating levels of ghrelin were compared between the two groups using two-sample t tests or Chi-square tests using MATLAB (Mathworks Inc. , Sherborn, MA). Two subjects from the control group and 1 subject from the obese group did not properly follow instructions for the performance of the guessing task during the MRI acquisition. Therefore, only data related to ghrelin levels and anatomical brain images were used in those subjects. Cerebral BOLD responses during the fMRI task were assessed using a general linear model approach similar to the one described by Reuter and collaborators  (Reuter et al. , 2005). Briefly, for each subject, we set up a linear model with two regressors of interest corresponding respectively to the differential "gain vs.
Since the dlPFC turned out to be more activated in the obese group compared to controls, we focused on this region of interest (ROI), extracting the eigenvariates of parameter estimates of the "gain vs. loss" contrast using a bilateral spherical ROI of 6 mm radius around the peak of the group effect in dlPFC. The resulting values were then used to test the main and interaction effects between variables of interest: reward-related brain activation, levels of ghrelin and behavior in groups of healthy volunteers and obese subjects with ANCOVA analysis in MATLAB. We calculated the effect size and reported it as Cohen's d for betweengroup comparisons and the partial Eta Squared value, ƞ2p, for ANCOVA analysis.
While previous studies addressing reward processing alterations have shown that hedonically driven food intake, along with stress-induced comfort eating, may contribute to weight gain and obesity maintenance  (Burger and Berner, 2014; Lee and Dixon, 2017) , further large-scale longitudinal studies are needed to specifically address this issue. This study presents certain limitations that future investigations should also overcome. Due to logistic constraints inherent to clinical research on patients (ghrelin measurement was part of the routine preoperative evaluation of obese patients), ghrelin levels were not measured on the same day of the fMRI acquisition in 60% of the participants. While this limitation should not critically impact results from the present study, based on data from prospective studies showing stable fasting ghrelin levels with time in obese subjects  (Hanusch-Enserer et al.