dataesr/scientific-paragraphs-categorization huggingface dataset:
All 100 confusion matrices were collected and averaged to assess the risk of misclassification (and thus the degree of identifiability of the three categories). Finally, a permutation test was applied to assess the significance of the differences. To better investigate the differences among BF G-layers and G-layers of both poles, these analyses (PCA, HCA and PLS-DA) were repeated on three datasets: (i) the full dataset; (ii) a dataset excluding aromatic wavenumbers (1270-1421 cm -1 , and above 1510 cm -1 ), because these wavenumbers were found to differ between BF G-layers and xylem G-layers; (iii) a dataset excluding bast fiber G-layers, to focus on differences between xylem G-layers of both sides. PCA, HCA and PLS-DA were performed with R software (https://www. r-project. org/ using libraries ChemoSpec and mixOmics accessed on 20 December 2022)  [14, 19].
to cellulose (607-900 cm -1 ) and hemicelluloses (1729 cm -1 ) also showed higher intensities than corresponding bands in BFs. In order to further evaluate potential similarities/differences between xylem and BF G-layers, spectral data were analyzed by PCA (principal component analysis) (Figure  3 , Figure  S1 ). Given that no lignin was detected with the Wiesner Reaction in all G-layers, the term "aromatics" was used for the bands related to [a1: 1270 cm -1 ; a2: 1421 cm -1 ; a3-a4: 1599-1658 cm -1 ]. The PCA biplot (Figure  3A ) clearly showed that the PC1 (explaining 54% variability) axis separates the datasets into two clusters: xylem G-layers (red and green dots) and BF Glayers (blue dots). The left cluster contains xylem G-layers from the tension side (red dots) and the opposite one (green dots).
PLS-DA of Spectral Datasets Whether using the full dataset (Figure  4A ) or modified datasets (without aromatic bands; Figure  4B ), PLS-DA biplots (component 1 vs. component 2) clearly discriminated BF G-layers (blue) from xylem G-layers (green, red), notably along the PLS-DA 1 axis. The fact that BFs were still separated from xylem G-layers in the modified dataset (Figure  4B ) indicates that aromatics are not the only factor contributing to such a separation. The second axis PLS-DA 2 partially separated xylem G-layers from both wood sides, but overlapping was nevertheless observed. When trying to discriminate only xylem G-layers spectra (Figure  4C ), the PLS-DA was less successful. There were some misclassifications, and regardless of the dataset used, these misclassifications concerned almost only tension versus opposite xylem G-layers (Table  1 ).
PCA methodology allows the exhaustive characterization of the hyperspectral datasets  [42]. In this study, chemical imaging was performed after the PCA approach in order to restrict chemical imaging only to positive or negative contributions. In addition to its fundamental interest, a better understanding of cell wall remodeling in response to gravitropic mechanical stress is also of practical interest. In flax for example, the composition of bast fiber cell walls is greatly altered in the tension pole  [18] , thereby impacting their quality for textile uses. In conifer wood, stress-induced gaps between cell layers have been reported that could alter tensile properties, and the modification of the global sugar composition of lignified cell walls will affect bioethanol production (see references in  [16] ).
Funding: This study was funded by grants from the  French Region Hauts-de-France  and the  EU (CPER/FEDER  project  ALIBIOTECH ) and national  French Research Ministry  grant ( ANR-12-ADAPT-0011  NoStressWall). Institutional Review Board Statement: Not applicable. The study did not involve humans or animals. Informed Consent Statement: Not applicable. The study did not involve humans or animals.
Patients were systematically reassessed by a pediatric gastroenterologist 8 weeks later. Only if the T-fastener sutures were persistent after 8 weeks, were they removed and classi ed as a late drop of Tfastener. The rst button change was performed 4-6 months after the procedure, under medical supervision in our center. Patient characteristics (demographic data and history, endoscopic procedure, postoperative complications, and long-term outcome) were collected retrospectively from medical records. Patients' comorbidities were categorized as follows: neurological, gastroenterological, metabolic/genetic, pneumological/cardiological, oncological, oropharyngeal abnormalities, and prematurity (gestational age < 37 weeks). The indication for the PEG tube (nutritional support and aspiration prevention) was recorded.
Statistical Processing ANOVA, Multivariate analyzes of variance (MANOVA) and Pillai trace tests with a 95% confidence interval were carried out in order to assess the significance of the impacts of the factors studied on all the variables measured, and rank the influence of these factors. The significance of the differences between modalities was tested by SNK (Student-Newman-Keuls) tests within a 95% and 99% confidence interval. Correlation analyses allowed performing existing links between the different variables. Both SAS Software (SAS 9. 3 TS-Version windows 6. 2. 9200. SAS Institute Inc. SAS and all other SAS Institute Inc. , Cary, NC, USA) and R packages were used to perform these analyses: readxl, xlsx, FactoMineR, Ggally, agricolae, tidyverse and rlist R Studio (version 4. 0. 2).
Whole Grain Quality Criteria Three main criteria-thousand-kernel weight (TKW), specific weight (SW) and protein content (PROT)-usually considered in the case of durum wheat commercial contracts have been estimated on whole grains by NIRS. These estimates have been made on the whole grain samples of 4, 18 or 20 varieties according to the year. Five environments were considered: 3 years of harvest  (2016, 2017, 2019)  and, for some years, 2 farming systems (ZI and LI) or 2 different locations (Mauguio and Purpan). A classic ANOVA comparing the impact of the varieties and the impact of the environments on these data made it possible to define the contribution of each of the factors to the variability of the criteria (Table  3 ). Table  3. Average of the thousand-kernel weight (TKW), specific weight (SW) and protein content (PROT) measured on durum wheat whole grains by NIRS method, according to the year, the cropping system and the location.
Acknowledgments: The authors acknowledge the  DiaScope (Mauguio) INRAE  team for the grain production and NIRS analysis. The authors want to thank  Lycée Agricole d'Auzeville  and, mainly,  Arnaud Marcodini  for the milling and " Artisanal 2" pasta processing. They also want to thank warmly  François Caizergues  for the milling and " Artisanal 1" pasta processing.
Adapter sequences were trimmed, and all sequences were trimmed to a maximum length of 100 bp before alignment. The raw sequences were made using NCBI Sequence Read Archive before analysis with established pipelines. In terms of taxonomic classification, FASTA sequences were aligned making a curated database, which contained all representative genomes in the NCBI RefSeq, a representative genome collection for prokaryotes with additional manually curated strains for bacteria  [16]. Alignments were made at 97% identity and compared to reference genomes. Every input sequence was compared to every reference sequence in the Diversigen DivDB-Dog database using fully gapped alignment with BURST. Ties were broken by minimizing the overall number of unique Operational Taxonomic Units (OTUs). The input sequences were listed as the lowest common ancestor for taxonomy assignment, which was not compatible with <80% of the reference sequences.
OTUs accounting for less than one million of all species-level markers and OTUs with <0. 01% of their unique genome regions matching as well as <0. 1% of the whole genome were discarded. The average sequencing depth was 2. 3 ± 0. 8 million (mean ± standard deviation) reads per sample. For downstream analysis, normalized and filtered tables were used in QIIME2  [17]. The OTU tables were rarified at 158,023 sequences per sample, which was the lowest read of the samples. Alpha diversity was evaluated by the number of species, Shannon-Wiener index, and Chao1 index, and observed operational taxonomic units (OTUs) using the rarefied OTU table. Beta diversity was evaluated by principal coordinate analysis (PCoA) plots using the Bray-Curtis dissimilarity. KO groups were observed with alignment at 97% identity against a gene database derived from the NCBI RefSeq representative genome collection for prokaryotes with additional manually curated strains for bacteria mentioned above for functionally annotated genes  [18, 19].
Calculations and Statistical Analysis Based on the laboratory results, the coefficients of total tract apparent digestibility (ATTD) and the diet metabolizable energy (ME) were calculated according to  [20] : ATTD (%) = [(g of nutrient intakeg of nutrient excretion)/g of nutrient intake] × 100. ME (kcal/kg) = {kcal/g GE intakekcal/g GE fecal excretion -[(g CP intakeg CP fecal excretion) × 1. 25kcal/g]}/g of feed intake. Main statistical analyses were performed using Minitab ® (version 19. 2020. 1) software. Each dog was an experimental unit. Yeast supplementation and sex were treated as fixed effects; the day of measurement was treated as a repeated measure. Observations that were at least 1. 5 times the interquartile range were considered as possible outliers. A Grubbs' test was performed for confirmation if only one possible outlier was detected.
If more than one possible outlier was detected, a Rosner test was performed using the function "rosnertest" from package "EnvStats" (Millard 2013) with R software (version 4. 0. 2). An analysis of variance (two-way ANOVA) was performed, using the function General Linear Model, to assess the effects of supplementation and interaction with the day of measurement. Normality and homoscedasticity assumptions were visually checked using residuals plots. Data were log-transformed if residuals were not uniformly distributed. Fisher LSD with Bonferroni correction was applied as post hoc test. Statistical significance was defined as p value < 0. 05 while p < 0. 10 was considered a trend. Alpha diversity metrics for the microbiome results were evaluated by Chao1 and Shannon indexes using QIIME2 v. 2021.
2. Beta diversity, using Bray-Curtis distances, and its plots were analyzed and generated using Past software 4. 03. Analysis of similarity (ANOSIM) was used to evaluate the similarity of the microbiota and KO terms between groups at different time points. Differential abundance of KEGG Modules and KO terms between control and probiotic groups on days 21 and 49 and between diets (day 21 vs. day 49 regardless of the treatment group) was analyzed using linear discriminant analysis (LDA) effect size (LEfSe) on MicrobiomeAnalyst according to  [21]. KEG Modules and KO terms with log LDA score higher than 2 and adjusted p < 0. 05 for false discovery rate were considered significant.
WXMS presented an average granule diameter within the expected range (2-30 µm) for corn starches  (Charles et al. , 2005). DIAZ, A. P. et al. Table  2  provides the summary statistics for granule size distribution, what stands out in the presented data is that WXCS highest percentage (>66%) was between 10 and 20 µm, and the WXMS was close to 60% for the same interval. When the size distribution was analyzed by percentile, 90% of WXCS granules had a diameter smaller than 25. 10 ± 0. 49 µm. For all size distribution limits (percentile), WXMS granules were always smaller than WXCS granules, and these physical differences were confirmed by scanning electron microscopy. Waxy cassava starch granules (Figure  2 ) presented elliptical, kettledrum or spherical truncated shapes, and some damaged granule particles were observed, probably as a result of damage by the mechanical extraction process.
Cecal SCFAs Quantification Cecal content samples (10 mg) were homogenized using Precellys in 0. 5 mL of a 5 mM NaOH solution containing internal standards (Acetate-D3, Propionate-D2, Butyrate-13C2 and Valerate-D9). Super-natant (300 µL) was mixed with 500 µL propanol/pyridine solution (3:2 v/v). SCFAs were derivatized using isopropylchloroformate and extracted using 0. 5 mL of hexane. Quantification of SCFAs was performed with a gas chromatograph coupled to a mass spectrometer (ISQ LT, ThermoFisher Scientific, Waltham, MA, USA) and XCalibur QuanBrowser software 4. 2. (ThermoFisher Scientific).
Reverse transcription and real-time quantitative PCR One microgram of extracted RNA was retrotranscribed using the SuperScript TM VILO TM cDNA synthesis kit (Thermo Fisher, Waltham, MA, USA) according to the manufacturer's instructions. Quantitative PCR (qPCR) was performed on retrotranscribed products using the Mastercycler ep Realplex (Eppendorf, Hamburg, Germany). The reaction conditions consisted of 15 min at 95°C (1 cycle), 15 s at 95°C and 60 s at 60°C (45 cycles) with primers using ABsolute QPCR SYBR Green (Thermo Fisher, Waltham, MA, USA). Samples were analysed in triplicate using GAPDH and CPR2 as housekeeping genes. The primers used in this study as well as restriction efficiencies are listed in Table  S1. PCR-primer pairs were designed from mRNA sequences of the studied genes provided by the National Center for Biotechnology Information (NCBI) gene database using PrimerBlast.
A negative control was present on each slide with secondary antibody only. Slides were washed as previously described and mounted using Vectashield + DAPI to stain nuclei blue. Slides were observed on an epifluorescence microscope, x40 magnification, with a DAPI filter to visualize nuclei and a FITC filter to visualize potential infiltrating immune cells. The infiltrating cell rate was measured by cell counting using ImageJ software  [33].
Bioinformatics and statistical analyses Bioinformatics and statistical analyses were performed using a home-made pipeline according to  [35]  and  [35, 37, 37]. Quality checks and trimming were performed using TrimGalore v0. 4. 5, which removed adapter sequences, poor quality bases and reads (Phred score below 20), and reads shorter than 20 nucleotides. High-quality reads were aligned to the mouse reference genome GRCm38 primary assembly (Ensembl 100) using Bismark_v0. 20. 0  [38] , which uses Bowtie 1. 2. 1. 1 alignment software  [39]. The bisulphite conversion rate was estimated from the unmethylated cytosine added in vitro during the end-repair step and was ≥ 99. 5%. The CpGs were then selected based on their coverage by uniquely mapped reads. Around 1,273,950 CpGs covered by at least 10 uniquely mapped reads (CpG10) were retained for subsequent analyses.
A DMR was constituted by a minimum of three DMCs with a maximum inter-DMC distance of 100 bp. The annotation of the DMCs, DMRs, and the 'background' was performed as described in  [36, 36]  relative to gene features, CpG density, and repetitive elements using an in-house pipeline. The reference files were downloaded at the following sites: http://ftp. ensembl. org/pub/release-100/ gtf/mus_musculus/Mus_musculus. GRCm38. 100. gtf. gz, http://apr2020. archive. ensembl. org/bio mart/martview/db614f58c20a42c0d2cb13b cedf364f8 [Ensembl Genes 100, Mouse genes (GRCm38. p6)], http://hgdownload. soe. ucsc. edu/ goldenPath/mm10/database/cpgIslandExt. txt. gz and http://hgdownload. soe. ucsc. edu/goldenPath/ mm10/database/rmsk. txt. gz. The following criteria were applied: transcription start site (TSS), -100 to + 100 bp relative to the TSS; promoter, -2000 to + 100 bp relative to the TSS; transcription termination site (TTS): -100 to + 100 bp relative to the TTS; shore, up to 2000 bp from a CpG island (CGI); and shelf, up to 2000 bp from a shore.
A site/fragment was considered to belong to a CGI (respective shore and shelf) if an overlap of at least 75% was observed between the site/ fragment and the CGI (respective shore and shelf). A site/fragment was considered overlapped by a repetitive element, regardless of the extent of this overlap. DMCs were subjected to enrichment analyses with the Database for Annotation, Visualization, and Integrated Discovery (DAVID) using the 'background' as a reference genome  [41, 42].
Inflammation induces gene expression changes in mammary tissue To determine the effect of inflammation on mammary gland function, we analysed the expression of 63 genes via RT -qPCR. In total, there were four differentially expressed genes (DEGs) out of 20 genes involved in mammary gland development and function, 5 DEGs out of 13 genes involved in epigenetic regulation, 11 DEGs out of 27 genes involved in the immune response, and 3 housekeeping genes (Figure  1 ). The abundance of the housekeeping genes was similar across all samples and did not vary with lactation rank and the presence of inflammation (data not shown). S2.
Covariates Covariates were selected as controls for empirical and theoretical reasons  (22) (23) (24). When children were 5 months old, the person most knowledgeable about the child (99. 0% were mothers) provided data on the household income (<30 K CAD/year vs. higher income), maternal education (university diploma vs. no university diploma), if the mother was an immigrant (yes/no), maternal age, and family composition (single-parent, two-parent, or stepfamily). Birth weight (<2,500 g) and developmental/stunted growth (<10 th centile) of the child were derived from the birth medical registry. The mothers also reported if they worked since pregnancy (yes/no). Maternal smoking during pregnancy was coded present if the mother had smoked at least one cigarette/day while pregnant. Prenatal alcohol exposure was coded as 0 = never, 1 = having drunk alcohol less than 3 times/month.
Funding The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The  Quebec Longitudinal Study  of Child Development was supported by funding from the  ministère de la Santé et des Services sociaux, the ministère de la Famille , and the  ministère de l'Éducation et de l'Enseignement supérieur , the  Lucie and André Chagnon Foundation , the  Institut de recherche Robert-Sauvé en santé et en sécurité du  travail, the  Research Centre of the Sainte-Justine University Hospital , the  ministère du Travail de l'Emploi et de la Solidarité sociale , and the  Institut de la statistique du Québec. This study was also supported by the  Canada Research Chairs Program.
Purpose: In patients presenting with hypertrophic pyloric stenosis, the placement of a nasogastric tube (NGT) before surgery is supposed to prevent the aspiration of gastric uid into the lungs. The objective of the present study was to determine whether or not a NGT prevents respiratory complications. Methods: A cohort of 87 patients from a prospectively maintained database were retrospectively included in the study; we compared patients with vs. without NGT placement before surgery. The primary endpoint was the occurrence of respiratory complications. Results: Three patients (two patients in the no-NGT group and one in the NGT group) presented severe respiratory complications; even though there was no evidence of lung aspiration, these adverse events obliged us to discontinue the study. There were no differences between the NGT and no-NGT groups with regard to the time to correction of the electrolyte imbalance, the time to complete oral refeeding, the length of hospital stay, and the incidence of other complications.
Methods We included patients recorded in our university medical center's prospectively maintained database. The patients' demographic data were collected. All patients had a con rmed diagnosis of HPS after a clinical examination and an ultrasound scan. The study's main exclusion criteria were concomitant respiratory or cardiac disorders, a respiratory complication at diagnosis, and refusal of data collection and use by the patient's parents or legal guardian. All patients were admitted directly from our emergency department or indirectly from other medical centers. All patients underwent laboratory tests (electrolyte imbalance, hemostasis, etc. ). The intravenous electrolyte correction began as soon as HPS was diagnosed. The patients were monitoring in a pediatric intensive care unit, in accordance with our institutional practice.
The study was approved by an institutional review board (CPP Nord Ouest II, Amiens, France; reference: PI2021_843_0188) and was registered at ClinicalTrials. org (NCT05068622). Statistical analyses were performed with GraphPad Prism software (GraphPad Software LLC, San Diego, CA). Quantitative variables were expressed as the median (range), and groups were compared in a chi-squared test or (for small sample sizes) Fisher's exact test. Student's t-test was used to compare categorical variables.
Supplementary Method 3. Methodology for food additives/artificial sweetener intake assessment Artificial sweetener intake of each participant was evaluated through the 24h-dietary record tool which collects information on brands and commercial names of industrial product. The methodology for food additive exposure in the NutriNet-Santé cohort has been described in details elsewhere  (6). Qualitative information on presence or absence of each food additive in each specific food/beverage consumed was obtained from 3 large-scale composition databases: the French food safety agency (ANSES) and National Research Institute for Agriculture, Food and Environment (INRAE) database Oqali  (7)  (https://www. oqali. fr/oqali_eng/), Open Food Facts (https://fr-en. openfoodfacts. org/) (8) [OFF] and Mintel's Global New Products Database [GNPD]  (9).
Regarding the specific case of artificial sweeteners, only aspartame, acesulfame-K and sucralose were consumed by more than 10% (all others were consumed by less than 3. 5%). In the present study, all artificial sweeteners consumed contributed to the total artificial sweetener intake, but specific analyses for single substances were only conducted for aspartame, acesulfame-K and sucralose to allow sufficient statistical power. The accuracy of the qualitative and quantitative food additives exposure assessment of the NutriNet-Santé cohort represents an important strength of the study, thanks to detailed and repeated 24h-dietary records, linked to multiple food composition databases (OQALI  (7) , Open Food Facts (8), GNPD  (9) , EFSA  (11) , and GSFA (10)), ad-hoc laboratory assays, and dynamic matching to account for reformulations of industrial food items over time  (6).
Supplementary Method 4. Methodology for type 2 diabetes ascertainment Participants were asked to declare major health events though the yearly health questionnaire, through a specific health check-up questionnaire every six months, or at any time through a specific interface on the study website. They were also asked to declare all currently taken medications and treatments via the check-up and yearly questionnaires. A search engine with embedded exhaustive Vidal® drug database is used to facilitate medication data entry for the participants. Besides, our research team was the first in France to obtain the authorization by Decree in the Council of State (n°2013-175) to link data from our general population-based cohorts to medico-administrative databases of the National health insurance (SNIIRAM database).