dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2018; Filipović Marijić et al. , 2018). Sampling was conducted by electrofishing, in accordance with the Croatian standard legislation for fish sampling by electric current power  (HRN EN 14011, 2005). In total 13 fish individuals were sampled, all of which were infected with 269 acanthocephalans, resulting in a mean intensity of infection 20. 7 ± 8. 9. Detailed data on fish biometry and the epidemiological characteristics of the acanthocephalans can be found in  Mijošek et al. (2022). Captured fish were kept alive in aerated water until further processing in the laboratory. After trout were anaesthetized and killed with tricaine methanesulfonate (MS 222 Sigma Aldrich) in accordance with the Regulation on the Protection of Animals Used for Scientific Purposes (NN 55/ 2013), the gastrointestinal tract (stomach, pyloric caeca, and the anterior, middle and posterior parts of the intestine) was removed and opened along its entire length and carefully examined for intestinal parasites.
Inner surface of the tegument In addition, NanoSIMS provided the first data on the elemental distribution in the ultrastructure of the inner surface of the tegument of D. truttae (Fig. 7 ). The inner layer of the acanthocephalan tegument also had higher concentrations of S, Na and Ca than the circular and longitudinal muscles. Sulphur and Na were localised mainly in the contractile filaments of the muscle, whereas Ca was found mainly in the central cytoplasmic core of the longitudinal and neck retractor muscles (Fig. 7 ). Sodium was also partially present in the same areas and had few hotspots in the neck retractor region (Fig. 7 ). Of the other elements measured, only Fe and P were observed in the circular and longitudinal muscles. Similar to the trunk spines (outer tegument), Fe and Cu were the predominant metals in the inner tegument of acanthocephalans, while Se (not shown), Tl and Pb were also not detected in this part (Fig.
Acknowledgements The authors thank the  Czech Science Foundation  (project No. 19-28399X ) and the  Czech Academy of Sciences  (RVO:  60077344 ) and are sincerely grateful to the  Bordeaux Imaging Centre  (member of the  France BioImaging national infrastructure ,  ANR-10-INBS-04 ) for help with TEM and to members of the  Laboratory of Biological Effects of Metals and Laboratory of Aquaculture and Pathology of Aquatic Organisms  ( Ruđer Bošković Institute, Croatia ) for the assistance with fieldwork.
Thus, measuring the AX content can be used to estimate TDF content in WB. In the absence of tangible and reliable data based on clinical studies to predict and clearly explain physiological effects by DF solubility, FAO/WHO have recommended the phasing out of the distinction between soluble and insoluble fibres. However, this solubility-based classification is still widely used, as SDFs constituted of non-cellulosic polysaccharides (e. g. , pectin, gums, psyllium, mucilage) are being increasingly used and studied. In addition, these water-soluble fibres are showing effectively physiological effects.
Cholesterol Adsorption Capacity Cholesterol adsorption capacity (CAC) is the ability of wheat bran to bind cholesterol molecules. It is determined by a colourimetric method which serves to assess the adsorption of lipophilic substances by the sample. The pH seems to play a role in the CAC  [63] ; CAC is around four times lower at pH 2 compared to pH 7 (Table  4 ). Data suggest that interactions between DF and cholesterol molecules are not based on ionic bonds. Both are positively charged in acidic environments, leading to repulsion phenomena. Neutral pH corresponds to the small intestine environment and acidic pH to the stomach environment. This indicates that WB can potentially adsorb more cholesterol in the small intestine than in the stomach. There is a positive correlation between SDF content and higher ability to adsorb cholesterol  [140].
Biochemical analyses Gas chromatography was used to measure acetate, propionate, isobutyrate, butyrate, isovalerate, valerate, and phenol levels in cell-free supernatant samples of the KO strains and their respective WT strains, as described previously. 52  Data were collected from three independent bacterial cultures. SCFA analysis in the cecal contents was also performed by gas chromatography as described by Lan et al. ,  53, 54  with slight modifications. Samples stored at -80°C were thawed at room temperature and extracted with water. Proteins were precipitated with phosphotungstic acid. A 0. 3 µL volume of the supernatant was injected onto a gas-liquid chromatogram Agilent 6890 (Agilent Technologies, Courtabeouf, France) equipped with a split-splitless injector, flame-ionization detector, and capillary polyethylene glycol column (15 m × 0.
53 mm, 0. 5 µm). The carrier gas (H 2 ) flow rate was 10 mL/ min, and inlet, column, and detector temperatures were 200°C, 100°C, and 240°C, respectively. Between each sample injection, the column was cleaned by increasing the temperature from 100°C to 180°C (20°C/min) followed by holding at 180°C for 2 min before returning to 100°C for the next analysis. We used 2-ethylbutyrate as an internal standard. Samples were analyzed in duplicates. Data were collected and peaks integrated with the OpenLab CDS Chemstation Edition software (Agilent).
Statistical analyses For each Clostridium species, the proportions of quails exhibiting NEC-like lesions in the WT and KO groups were compared using Fisher's exact test. For the other parameters of the animal experiments, the Mann-Whitney U was used. For the phenotypic comparison of the data from the different strains, Welch's two-sample t-test (two-sided) was used. Calculations were performed with GraphPad Prism software (v. 7. 03, La Jolla, CA, USA). Statistical significance was set at P ≤. 05.
Cell Counting Operations For cell counting operations, we used a Nikon Eclipse Ti-U fluorescence inverted microscope (Nikon France, Champigny sur Marne, France) equipped with an ORCA-Flash digital camera (Hamamatsu Photonics, Massy, France) and the NIS-Elements software Version 5. 41 (Nikon). The number of TH + neurons was estimated by visually inspecting with a 10× objective 10-15 visual fields that were randomly selected for each treatment condition.
Survey participants and recruitment The study targeted two categories of people: (i) those involved in the KC of a preterm child born in the six months preceding the survey, i. e. , the parents or other family members participating in KC, and (ii) the health personnel of the seven selected BHCs. The parents and family members interviewed were recruited from the registers of the selected BHCs. The determination of gestational age remains challenging, due to both a lack of data on gestational age at birth in the BHC registers and the non-availability of ultrasound devices. Therefore, infants with a low birth weight (LBW) were rst identi ed from the registers and then, in collaboration with community workers, the selected mothers were interviewed to determine whether their children were born preterm.
Type of data collected and entered In total, 54 interviews were conducted, including 32 with mothers of preterm infants and/or family members practicing KC, and 22 with healthcare professionals (3 doctors, 16 midwives, 3 nurses) involved in KC. In addition, we conducted two focus groups with parents of preterm infants, focusing on the themes that emerged from the semi-structured interviews, to examine the consistency of the responses given. Those practicing KC were interviewed at home, whereas care staff were interviewed at the BHCs. The interviews were conducted in Malagasy. They were recorded and then transcribed in their entirety into a Word le. The interviews were then translated, in their entirety, into French.
Analysis This survey responds to a need expressed by the Ministry of Public Health in Madagascar to test the possibility of scaling up the method in a community setting. The themes addressed are therefore intended to meet this need. A thematic analysis was used for data processing. The interviews were coded according to a list of codes established before data collection, with a code being the label used to mark a concept (for example: the care path during pregnancy). Coding was conducted by the rst author of this article. Coding is the rst step in the analysis of qualitative data. A cross-sectional thematic analysis was performed on the translated data by lling in an analysis grid. Two analysis grids were designed for this study: one for the interviews with the mothers of preterm infants and the other for the interviews with healthcare professionals.
Following washing with TBS-T (3 × 5min), membranes were incubated with an enhanced chemiluminescence (ECL) development reagent (Clarity Western ECL substrate, Biorad, UK) for 3 min and visualised by (ChemiDoc XRS, BioRad, UK), and band intensities quantified using ImageJ software normalising expression to GAPDH. Primary antibodies recognising human proteins used were: Caspase 3: rabbit polyclonal 9662 (Cell Signalling Technology (CST), UK), ATG5: rabbit polyclonal 2630, (CST), H3K4me3: rabbit polyclonal PA517420 (Thermo, UK), H3K27me3: rabbit polyclonal PA531817 (Thermo, UK), H3K9me2: rabbit polyclonal (CST), H3 (1B1B2): mouse monoclonal 14269 (CST) and GAPDH mouse monoclonal sc-47724 (Santa Cruz, UK), Bcl-2 rabbit polyclonal ab196495 (Abcam, UK), p21(CDKN1A): rabbit monoclonal 2947 (CST) and β-actin rabbit polyclonal 4967 (CST) were used at a concentration of 200 μg/ml overnight at 4 • C.
Blots were washed and then incubated with the appropriate secondary antibodies (goat anti-mouse ab150113 (Abcam, UK) or goat anti-rabbit ab6721 (Abcam, UK HRP secondary) at a concentration of 400 μg/ml. Immunoreacting proteins were visualised (ChemiDoc XRS, BioRad, UK), and band intensities were quantified using ImageLab software normalising expression to GAPDH.
RNA-sequencing For each condition, a total of 96 independently cultured spheroids were pooled. Extracted RNA from pooled samples underwent quality control assessment using the RNA Tapestation 2200 (Agilent). cDNA libraries were prepared using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen) prior to RNA-sequencing (RNA-Seq, genomic platform, Ecole Normale Supérieure de Lyon). Raw Fastq files were quality-checked using FastQC, a quality-control tool for high throughput sequencing data, prior to alignment to the hg38 indexed transcriptome using Bow-tie2  [14]. The eXpress software  [15]  was used to quantify expression from the transcriptome mapping and derive count data and the differential expression tool package DESeq2  [16] , implemented within R, was used to correct for multiple hypothesis testing and determine significantly modified transcripts (FDR <0.
1) (Supplementary 1). Raw and processed RNA-Seq data is deposited in the GEO Dataset with accession number GSE149397. All major PANTHER terms were tested for over-representation (GO-Biological Processes or Reactome, e. g. binomial) and gene-set enrichment by comparing the lists of genes expressed in different experimental conditions. The results are displayed showing the differential distribution of significantly enriched clusters of genes compared to the overall expression tendency within samples. The Database for Annotation, Visualization and Integrated Discovery (DAVID; https://david. ncifcrf. gov/) was used to provide functional annotation of gene lists and results displayed with Fisher's Exact test used to measure the gene-enrichment in annotation terms.
High energy resolution fluorescence detected X-ray absorption spectroscopy Energy Resolution Fluorescence Detected X-ray Absorption Spectroscopy (HERFD-XAS) was used to determine Se speciation. Measurements were performed on FAME-UHD beamline at the European Synchrotron Radiation Facility (ESRF, Grenoble, France) at the selenium K-edge (12658 eV). The samples were analysed at 10 K to avoid radiation damages using a crystal analyzer spectrometer (CAS) equipped with 6 Ge(844) bent crystals (1 m radius of curvature), allowing an energy bandwidth for the fluorescence detection around 3. 3eV. Data analysis was performed by linear combination fitting of the so-obtained spectra using a set of model compounds spectra previously measured obtained on the same conditions  [18].
65, SeNP-BSA 0. 56, SeNP-chitosan 0. 87) compared to the control (0. 46) that was only significant for SeNP-chitosan (p < 0. 05). Data represent the mean ± SD of three biological replicates *p < 0. 05 significant vs respective Control (untreated) for each treatment. To determine nanoparticle penetration, SKOV-3 cells were treated with FITC-tagged-SeNP-BSA for 24 h (d). Confocal microscope (Ex 495 nm/Em 521 nm) imaging shows 50 μm z-stacks of a 300 μm diameter spheroid (scale bare 100 μm). Local fluorescence was observed inside the spheroid demonstrating nanoparticle penetration. GSSG/GS-Se-SG ratios were observed in response to SeNP treatment in both OVCAR-3 (Fig. 4E ) and SKOV-3 cells (Supplementary Fig. S3 ). SeNP treatment also resulted in an anticipated increase in thioredoxin reductase 1 (TrxR1) expression, which catalyses the conversion of SeO3 ( 2-) to H2Se (Fig.
Specifically, a core set of genes that were regulated by all three selenium treatments (Supplementary Fig. S6A , Table  S1 ) and in both cell types were identified (Supplementary Fig. S6 B , Table  S2 ) and revealed that as well regulating genes involved in oxidative stress including thioredoxin reductase 1 (TXNRD1), selenium also influenced biological pathways and processes including cell adhesion, metal ion binding and protein phosphorylation (Table  1 ). Consistent with the model for epigenetic regulation, chromatin remodeling was also an enriched term. To understand the relationship between histone methylation and the expression of apoptotic genes, we performed the analysis of publicly available SKOV-3 ChIP-Seq datasets  [19]. Using this approach, we identified persistent H3K27me3 peaks surrounding the proximal and/or core promoter regions of both Bcl-2 and p21 (Supplementary Table  3 ) suggesting a direct link between histone methylation and the regulation of apoptotic genes.
Acknowledgements Benoit Toubhans received a scholarship co-funded by the  Université Grenoble Alpes  and  Swansea University. Nour Al Kafri received a  postgraduate development fellowship  from the  Council for At-Risk Academics (CARA). We recognise  CEMHTI (Orleans, France ,  ANR-13-BS080012-01 ) and  Labex OSUG@2020 (Grenoble, France ,  ANR-10-LABX-0056 ),  FAME-UHD (EquipEx (EcoX ,  ANR-10-EQPX-27-01 )) for beamtime. We thank  Drs L. Sauzéat ,  S. Bouchet  and  Pr. L. H. Winkel ,  ETH Zürich , for ICPMS and speciation analysis. The electron microscope image was supported by the  Rhône-Alpes Region, FRM ,  FEDER ,  CNRS ,  CEA , the  University Grenoble Alpes ,  EMBL ,  GIS-IBISA , the  Grenoble Instruct-ERIC Centre  (ISBG:  UMS 3518 CNRS-CEA-UGA-EMBL ) with support from  FRISBI  ( ANR-10-INSB-05-02 ) and  GRAL  ( ANR-10-LABX-49-01 ) within the  Grenoble Partnership for Structural Biology (PSB) platform  ( D.
Mineralogical characterisation and geochemical analysis Mineralogical characterisation was conducted using X-Ray Diffraction (XRD) conducted on the milled samples. Diffractograms were obtained at IRICA-UCLM with Bruker D8 Advance A25 equipment during a 15-min work programme. Measured patterns were qualitatively and quantitatively analysed with the Match v. 3 and the Fullprof software for Rietveld analyses, respectively  (Moore and Reynolds, 1997). Diffractogram interpretation focused on identifying the presence of quartz, Fe oxides and mineral phases containing Sb. Major and trace elements from the soil and biota samples were quantitatively determined by Energy dispersive X-ray fluorescence (EDXRF) using a Panalytical device (Epsilon 2 model). Each sample was analysed in duplicate during a 24-min run to perform four energy passes for the selected groups of elements.
, 2021). Data were expressed as μg TPF g soil -1 day -1. To study Sb leachability and bioavailability, modified BCR sequential extraction was carried out. This sequential extraction procedure (SEP) consisted in three successive extractions from which three extracts and the residual fraction were obtained. The methodology was based on the BCR method  (Quevauviller et al. , 1997) , adapted to a 4-step scheme as reported by, for instance,  Sahuquillo et al. (1999)  and  Delgado et al. (2011). Briefly, the different SEP steps allowed four fractions to be differentiated: the first fraction (F1), extracted by a solution of 0. 11 M acetic acid, releases the species that are soluble in water, easily leached by weak acids and associated with soluble carbonates; the second fraction (F2), extracted by 0.
Antibodies targeting intracellular cytokines were IFNγ (XMG1. 2) (Biolegend, Amsterdam, The Netherlands), IL-10 (JES5-16E3) (Life technologies, Courtaboeuf, France), and IL-17A (TC11-18H10) (BD Biosciences, Le Pont-de-Claix, France). After intracellular labeling, cells were fixed with FACS (fluorescence-activated cell sorting) Lysing Solution 1X (BD Biosciences, Le Pont-de-Claix, France) and stored at +4 • C until acquisition. All data were acquired on a BD Biosciences FACS Canto II and analyzed using FlowJo Software V10. 4. 2. The gating strategy is shown in Figure  S1.
The Thermal Mannequin The anthropomorphic, multisegment thermal mannequin was designed in our laboratory (Figure  1 ). It corresponds to a low-birth-weight neonate (simulated weight: 1500 g; body surface area: 0. 150 m 2 ) with a gestational age of approximately 30 weeks (according to Fenton et al. 's curves)  [25]  The body segments are articulated so that the posture to be modified. The mannequin is painted matte black, and its emissivity coefficient in the infrared (0. 97) is close to that of human skin. During the experiments, local temperature data were recorded with 18 thermistor probes (10 kOhms at 25 °C): 5 on the trunk, 2 on each of the limbs, and 5 on the head. The mean surface temperature was calculated by weighting the local surface temperatures according to the corresponding segment's relative surface area (trunk: 28%; head: 23%; lower limbs: 30%; upper limbs: 19%).
Under thermal equilibrium conditions (reached within 45 min), the electrical power supplied separately to the mannequin's six body segments makes it possible to control the corresponding surface temperatures and to take account of the body's thermal heterogeneity. The electrical power was measured using command-and-control software (Control Pro, Labtech, Wilmington, MA, USA) and corresponds to the heat transferred to the environment. When thermal equilibrium was reached, the electrical power was recorded and averaged over 30 min.
The mannequin is painted matte black, and its emissivity coefficient in the infrared (0. 97) is close to that of human skin. During the experiments, local temperature data were recorded with 18 thermistor probes (10 kOhms at 25 • C): 5 on the trunk, 2 on each of the limbs, and 5 on the head. The mean surface temperature was calculated by weighting the local surface temperatures according to the corresponding segment's relative surface area (trunk: 28%; head: 23%; lower limbs: 30%; upper limbs: 19%). Under thermal equilibrium conditions (reached within 45 min), the electrical power supplied separately to the mannequin's six body segments makes it possible to control the corresponding surface temperatures and to take account of the body's thermal heterogeneity. The electrical power was measured using command-and-control software (Control Pro, Labtech, Wilmington, MA, USA) and corresponds to the heat transferred to the environment.
Statistical Analysis The experimental conditions were studied in random order. Five measurements were made for each condition in order to assess the variability in the heat power supplied to the mannequin. In view of our comparisons of small samples, the effects of the thermal insulation of the coverings (a sheet alone vs. sheet + blanket at 20. 9 °C and at 25. 9 °C) were probed by applying nonparametric Mann-Whitney tests. The threshold for statistical significance was set to p < 0. 05. Quantitative variables were expressed as the mean ± standard deviation (SD). Statistical analysis was performed using Statview software (version 5. 0, Abacus Concepts Inc, Berkeley, CA, USA).
Statistical Analysis The experimental conditions were studied in random order. Five measurements were made for each condition in order to assess the variability in the heat power supplied to the mannequin. In view of our comparisons of small samples, the effects of the thermal insulation of the coverings (a sheet alone vs. sheet + blanket at 20. 9 • C and at 25. 9 • C) were probed by applying nonparametric Mann-Whitney tests. The threshold for statistical significance was set to p < 0. 05. Quantitative variables were expressed as the mean ± standard deviation (SD). Statistical analysis was performed using Statview software (version 5. 0, Abacus Concepts Inc. , Berkeley, CA, USA).
Firstly, the mannequin does not mimic convective and evaporative heat losses from the skin and the respiratory system, which have to be estimated mathematically (Equations (  2 ), (  3 ) and (  5 )). One of the determinants of skin evaporation is the fraction of body area that is wetted, which is based on a very old literature value from a study in adults  [30]. This value is probably an underestimate in neonates, whose thin skin lacks keratin and is very permeable to water vapor  [42]. Secondly, our model did not take into account changes over time in the thermal states of the mother and the neonate; we considered solely the variables known or assessed at birth. It would be interesting to measure changes over time in the skin temperature of the mother's trunk using infrared thermography. To the best of our knowledge, there are no literature data on these determinants of heat losses.
Label-free relative quantification of STEC proteins associated with the MFGM Approximately 40 μg of supplied proteins were prepared following instructions from the easyPep kit from Thermo Fisher Scientific. Samples were reduced and alkylated for 10 min at 95°C and then digested with LysC/Trypsin at a 1:10 ratio for 3 h at 37°C. Samples were then purified on the easyPep kit spin columns, dried, and taken up in 50 μL 0. 1% formic acid. The samples were then assayed by a fluorometric assay. The same quantity of each sample was analyzed on a highresolution orbitrap mass spectrometer in TOP20 HCD mode. MS data were reprocessed with Proteome Discoverer 2. 5 software (Thermo Fisher Scientific) with the Sequest HT search engine against (i) the total UniProt E. coli database (862,106 entries; October 2021), (ii) UniProt Bos Taurus database (37,539 entries; November 2021), and (iii) the proteomic sequences of the three STEC strains obtained from genomic sequences via NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (EDL933: 5,425 entries; 21765: 5,361 entries; PMK5: 1,994 entries) as well as the addition of a contaminant database, filtered at a false positive rate of 1%.
Quantification ratios between conditions were calculated by pairwise comparison and t-test directly in Proteome Discoverer software. The data presented in the study are deposited in the MassIVE repository, accession number MSV000090906. Further analyses were performed in R software (R Core Team, 2021) and the Venn diagrams were realized with the 'ggvenn' package  (Yan, 2022). To identify the proteins associated with the STEC extract, the proteins identified by MS/MS were filtered according to two conditions: (i) proteins were annotated to the Escherichia coli species and (ii) proteins were absent from the three biological replicates of samples not supplemented with surface proteins (PBS). Strain-specific differentially expressed proteins (DEPs) were extracted based on the values of the log2 abundance ratio <-1 or >1 (according to the order of the ratio) and a value of p <0.