dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical Analysis on Metabolic Analysis and Gene Expression Data Results are given as the mean ± SEM. Statistical analysis was performed using statistical software R (R Core Team). All data were tested for normality and homogeneity. Gene expression data were rank transformed before further analysis. Principle component analysis (PCA) was performed on the free amino acid dataset in search for biological clusters and outliers (R: factoextra  [58] ). One-way ANOVA was used to identify differences between Se treatments or sex. Tukey's HSD was used as a post hoc test in case a significant difference (p < 0. 05) was detected.
Bisulfite conversion was performed using EZ DNA Methylation-Direct Kit D5020, Zymo Research, but conversion reagent was used at 0. 9× concentration with incubation for 20 cycles of 1 min at 95 • C, 10 min at 60 • C and a desulphonation time of 30 min to increase the number of CpG nucleotides covered. Enrichment PCR was performed after AMPure XP clean up and library concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) and size distribution by a Bioanalyzer High Sensitive DNA Kit (Agilent). Sequencing was performed on Illumina HiSeq 3000/4000 instruments. The data have been stored in SRA  [59]  under the accession number PRJNA629594.
RRBS Data Processing Illumina2bam tools (1. 17. 3; https://github. com/wtsi-npg/illumina2bam) were used to de-multiplex pooled samples. SAMtools  [60]  was used to convert BAM files into FASTQ, before quality check by FastQC (Babraham Institute; https://www. babraham. ac. uk) and MultiQC  [61]. Adapters and low-quality reads in the RRBS mode based on Cutadapt  [62]  were removed with Trim Galore! (Babraham Institute). Long reads were trimmed to 50 bp, and reads were selected by in-house python scripts to keep only those digested by MspI and TaqI. Reads were aligned to the rainbow trout genome by Bismark  [63]  with Bowtie 1  [64]. Two Bismark tools, bismark_methylation_extractor and coverage2Cystosine, were used to retrieve methylation calls at CpG sites. Reads were filtered by methylKit tool  [65]  when either the number of reads was above 99.
Functional Annotation and Statistical Analysis of DMGs To find Kyoto Encyclopedia of Genes and Genomes (KEGG)  [70]  orthologues that correspond to rainbow trout genes, the results of BLASTKoala, GhostKoala  [71]  and KEGG Automatic Annotation Server (KAAS)  [72]  were merged. The precedence of BLASTKoala > GhostKoala > KASS was applied when conflicting annotation occurred. A total of 22501 orthologues along with 168 KEGG pathways were identified. Over representation analysis (ORA) on KEGG pathways and Gene Ontology (GO) terms  [73]  was performed on DMGs by the R package clusterProfiler  [74, 75]. The Wilcoxon signed-rank test (Wilcox) was used to test the differences of methylation rates between two groups in a pair-wise manner for KEGG pathways. A bootstrap version of the Kolmogorov-Smirnov test (KS-boot; the number of iterations: 1000) was used to test the methylation differences that are associated with a KEGG pathway against the methylation differences of the whole CpG sites in a region.
Acknowledgments: The authors wish to thank  P. Maunas  and  N. Turonnet  for the care of the fish and  F. Terrier ,  F. Sandres  and  A. Lanuque  for the preparation of diets. We are grateful to  M. Parailloux  for RNA extraction and qPCR analysis and the IMR technical staff for analytical assistance. We also thank  Amelie Nemc ,  Bekir Ergüner  and  Christoph Bock  at the  Biomedical Sequencing Facility at CeMM, Research Centre for Molecular Medicine (Vienna Austria ), for RRBS library preparation, sequencing and bi-sulfite read pre-processing.
Concerning the ATP7A protein, it is also deregulated in many cancers, such as in pancreatic cancer, where ATP7A is upregulated compared to that in chronic pancreatitis  [60]. The ATP7A protein plays an important role in the formation of metastases in breast cancer and induces the migration of vascular smooth muscle cells  [130]. In addition, high levels of ATP7A expression in primary tumors are associated with reduced survival according to publicly available databases  [131]. Finally, the family of copper-dependent LOX metalloenzymes has a role in tumor metastasis and fibrotic diseases. In the formation of premetastatic niches, cancer cells secrete the LOX protein to stimulate collagen cross-linking and fibronectin synthesis  [132]. This secretion promotes the migration and adhesion of tumor cells  [133, 134].
With the cytosol of the cells being a reducing environment, the Cu entering the cell will be reduced into its Cu(I) oxidation form. Such a release of Cu(I) will poison the cell  [189]. In the family of ionophores, several compounds such as docosahexaenoic acid (DHA), disulfiram (DSF), bis (thiosemicarbazone) copper complexes, and clioquinol can be found. The clinical use of clioquinol has been discontinued because of its neurotoxicity  [190] , but clioquinol or its analogues are still tested in combination or with different administration routes to maintain its anticancer effects while reducing toxicities  [191]. The anticancer efficacy of DSF was demonstrated in in vitro and in vivo models of inflammatory breast cancer  [192] , and DSF is currently tested in clinical trials (clinicaltrials.
gov id#: NCT04265274 and NCT03323346). In addition, the combination of DSF and DHA has been shown to promote the death of cancer cells and to reduce the growth of cancer cells in vitro and in vivo  [193]. One study has also suggested combining DSF with a PI3K inhibitor. This combination could be a new therapeutic strategy in breast cancer, particularly for patients with PIK3CA mutations  [194]. In addition, coadministration of this drug with copper has shown inhibition of tumor growth in hormone-sensitive and castration-resistant models of the disease  [195]. Finally, it has to be noticed that only the Cu-complexed form of these ionophores is active as a cancer treatment, i. e. , disulfiram (DSF), bis (thiosemicarbazone) copper complexes, and clioquinol, because the ligands alone (metal-free compounds) have a minimal anticancer effect  [196].
Methods Dietary intake of individual FA was estimated using centre-specific validated dietary questionnaires and the National Nutrient Database for Standard Reference of the United States. Circulating levels of 60 individual PL FA were measured in baseline venous plasma phospholipid samples in nested case-controls studies within the EPIC cohort (n = 9,996). The fatty acid composition in the phospholipid fraction was measured by gas chromatography in plasma samples. Spearman rank correlations were calculated to determine associations between FA intakes and plasma PL levels.
Interestingly, Extended X-Ray Absorption Fine Structure (EXAFS) experiments performed on a complex of UO2 2+ with an osteopontin fragment shows that a phosphorylated group is involved in the complexation of the metal ion. [35] re recently, the affinity of these two proteins for uranyl could be measured thanks to Capillary Electrophoresis coupled to Inductively Coupled Plasma Mass Spectrometry (CE-ICPMS). n another context, aiming at uranium recovery or extraction from sea water, a uranyl-binding protein has been de novo designed by computational screening based on the known scaffolds in the Protein DataBank (PDB). One protein that consists of three α-helices in a tight bundle demonstrates a particularly high affinity for uranyl  (10 12  ) with more than 10,000-fold selectivity over Ca 2+. [38] This metalloprotein design represents an important step toward developing strategies to extract uranium from the ocean.
Acknowledgements This research was supported by the  ANR   TURBO  (Grant  ANR-16-CE34-0003 ), the " Programme Transversal Toxicologie du CEA ", the  NRBC-E program , the  Labex ARCANE  (Grant  ANR-11-LABX-0003-01 ) and the  CBH-EUR-GS  ( ANR-17-.
Method We performed a bibliographic search on the Medline database, including articles published from January 1990 to August 2020. The following terms were combined: iron with metabolism, anemia, disorders, deficiency, overload, causes, consequences, biological tests and/or aged, or their equivalents. We also looked at one book on dietary reference intakes. This first literature search was supplemented by a bibliographic search related to specific aspects that we wanted to clarify (for example, to explain the interest of physical activity, especially in the elderly). The most relevant articles were retained for our bibliography.
Data represent mean ± SEM. (I) Aversive cold-plate test of mice coelectroporated with CIB1-FusionRed-RAB6a and EGFP (n = 6 animals) or CRY2-mCitrine (n = 10 animals). After room acclimation, animals were tested in a cold plate at 0 C (basal) and then were exposed to dark or blue light for 30 min before a cold-plate test. The time before aversive jump in seconds was quantified. An average of 3 trials on 3 different days was obtained for each animal. *p < 0. 05 by Friedman and Dunn's test. Data represent mean ± SEM. (J) Menthol-sensitized cold-plate test of mice coelectroporated with CIB1-FusionRed-RAB6a and EGFP (n = 6 animals) or CRY2-mCitrine (n = 6 animals). Coldresponse events of the electroporated left lower limb were monitored at 10 C after local application of menthol in the hindpaw, and an arbitrary score was assigned to the behavior: 0 indicated no response, 1 indicated a lifting response, and 2 indicated licking, brushing, or jumping.
STAR+METHODS Detailed methods are provided in the online version of this paper and include the following: d KEY RESOURCES TABLE d LEAD CONTACT AND MATERIALS AVAILABILITY activity at 33 C, which is increased by cooling of the recording solution. Voltage signals were amplified with an AC amplifier (A-M Systems 1800; gain 10,000; low cut-off 1 Hz; high cut-off 10 KHz). Data were captured at 33. 3 KHz with a Digidata 1322a interface, coupled to a computer running pClamp 9 software (Molecular Devices). Temperature was measured at the corneal surface using a BAT-12 microprobe thermometer (Physitemp) supplemented with an IT-18 thermocouple, and acquired simultaneously with voltage signals. Trigeminal ganglia and DRG neuronal cultures Animals were euthanized by exposure to CO 2 and decapitated. Trigeminal neurons were cultured as described previously  (Madrid et al.
Calcium imaging For ratiometric Ca 2+ imaging experiments, HEK293 stably expressing TRPM8-myc cells and HEK293 transiently transfected with TRPM8-YFP were incubated with 5 mM Fura-2 AM (F1221, Thermo Fisher Scientific) dissolved in standard extracellular solution supplemented with 0. 02% Pluronic (P6867, Thermo Fisher Scientific) for 50 min at 37 C in darkness. Fluorescence measurements were made with an inverted Nikon Ti microscope fitted with a 12-bit cooled ORCA C8484-03G02 CCD camera (Hamamatsu). Fura-2 was excited at 340 and 380 nm at 0. 5 Hz with a Polychrome V monochromator (Till Photonics), with exposure time no longer than 40 ms, and the emitted fluorescence was filtered with a 510 nm long-pass filter. Calibrated ratios were displayed online with HCImage version 2 software (Hamamatsu).
Morphology analysis of secretory structures Analysis of particles in the axonal compartment was carried out using a local maximum algorithm developed in MATLAB R2012a (Mathworks). Briefly, particles were segmented using a binary mask considering the fluorescence intensity of each structure relative to its surroundings. A minimum threshold of 40 arbitrary units (a. u. ) (range 1-255 a. u. ) and a minimum intensity difference of 35 a. u. (particle/surrounding) were used. Segmented images were analyzed using ImageJ (NIH). Number and area of particles were obtained using the same tool.
Colocalization analysis Co-localization analysis was performed as described previously  (Ramı ´rez et al. , 2010). Briefly, samples were acquired on a confocal microscope (Fluoview FV1000) using a UPLSAPO 60x/1. 35 NA objective, 4x digital zoom and KALMAN 2. An average of 10 confocal images per sample were considered in the analysis (0. 2 mm thickness each). We guaranteed that images did not saturate and that image background was slightly above zero. Image stacks were deconvolved with Huygens Scripting Software (SVI, Hilversum, The Nertherlands) using an algorithm based on the classic maximum likelihood estimator (CMLE). The signal-to-noise ratio was adjusted until the deconvolved images were free of pixel noise. Images were segmented using IDL Workbech 7. 0 (ITT Visual Information Solutions, USA).
ACKNOWLEDGMENTS We thank  Romina San Juan  for technical support in animal care supervision. We also thank  Cathy Jackson  ( Institut Jacques Monod, France ) for providing GBF1 constructs. This work was supported by  FONDECYT   3160725  (to V. H. C. ),  3160666  (to C. G. ),  1161733  (to R. M. ), and  1170307  (to A. C. ); by  DI-CYT-USACH   021843PP  (to M. P. ); and by the  Iniciativa Cientifica Milenio, Biomedical Neuroscience Institute  ( ICM P09-015-F  to A. C. ) and the  Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD)  (to R. M. and M. P. ). R. M. also thanks the support of  VRIDEI-USACH.
Clinical Data Maternal data were prospectively collected in an Excel file and included age, gestational age at delivery (GA), type of pregnancy, mode of birth (caesarean or vaginal), smoking status, and prior breastfeeding experience. Since milk from several days was pooled into batches, day of milk collection used for analysis was the average of the first and last days of collection. The daily milk volume produced by each mother was recorded in the designated milk management sheet. For neonates, birth weight and weight percentile were also recorded in the Excel file. Small for gestational age infants (SGA) were defined by birth weights below the 10th percentile on the female Fenton growth curve (https://peditools. org/fenton2013/index. php).
Statistical Analysis Statistical analyses were performed by the Minitab ® 18 software (Statistical Solutions, Kaysville, UT, USA). Descriptive statistics were calculated for all variables. Mothers were separated into three groups by maternal age: mothers below 30, mothers between 30 and 35, and mothers greater than 35 years of age. When considering multiple pregnancies, twins or triplets were classified as SGA if at least one infant fell below the 10th percentile on the Fenton growth curve and were only counted once. Average volume was divided into quartiles. GA was categorized into three groups: very premature (<32 weeks), moderately premature (32-36 weeks), and at term (>37 weeks). Lactation period was classified into four stages: first week, second week, third week, and greater than three weeks.
Population Characteristics Forty mothers completed the study, providing 102 milk samples. The descriptive characteristics of the study population are shown in Table  1. Of the 40 mothers who participated in the study, 33 delivered 39 preterm infants (≤28 weeks, n = 4; 29-31 weeks, n = 13; 32-36 weeks, n = 17). There were six mothers who delivered multiple pregnancies, representing 15% of mothers in the sample. Data are mean ± standard deviation (SD) or n (%).
How to Assess Food Intakes? In patients undergoing nutrition assessment, quantifying intakes is important as intake evaluation is now part of the GLIM definition of malnutrition  [12]  and influences nutritional care. This evaluation can be easily done by a trained dietitian or physician but is time-consuming. Many technology-based dietary assessment tools exist, relying on self-reported dietary intakes and using either text or images to help identify foods. A majority integrates databases to estimate energy and protein intakes. We are not aware of any work evaluating that type of tools in liver diseases. However, we believe their use could greatly improve nutritional care  [90]. A different approach of food intake would be to evaluate the appetite status by using a simple analogic visual scale  [91].
How to Follow Nutritional Status in Patients with Cirrhosis? Recent guidelines suggested a regular and appropriate follow-up for malnourished and/or sarcopenic patients  [22]. However, the way to follow these patients remains unknown. To our knowledge, no dedicated nutritional tool was specifically determined or studied for the follow-up of malnourished patients with CLD. Nevertheless, effects of nutritional interventions have been appraised with various parameters in recent studies. In a work by Roman et al. , patients with cirrhosis practicing physical activity 3 days a week for 12 weeks were followed. Functional capacities significantly increased after exercise. No difference in weight was found between the exercise and the relaxation groups. Anthropometric data did not correlate with changes in muscle mass.
Data Collection Data were collected on twenty traits including five qualitative (vigour at seedling. panicle exertion, panicle type, panicle leaf attitude and grain color) and 15 quantitative (plant height, number of internodes per plant, number of leaves per plant, leaf length, leaf width, culm diameter, days to 50% maturity, raceme length, number of racemes per panicle, number of grain par raceme, panicle.
Data Collection Data were collected on twenty traits including five qualitative (vigour at seedling. panicle exertion, panicle type, panicle leaf attitude and grain color) and 15 quantitative (plant height, number of internodes per plant, number of leaves per plant, leaf length, leaf width, culm diameter, days to 50% maturity, raceme length, number of racemes per panicle, number of grain par raceme, panicle weight, shoot dry matter yield, grain yield. harvest index and thousand seeds weight) (Table  1 ). These data were recorded following the Bioversity International rice descriptors list  [27].
Data Analysis Descriptive statistics were used to depict variations that emerge from qualitative and quantitative traits. When conditions are met, analysis of variance was performed for quantitative traits in order to firstly verify differences among accessions from various provenances and thereafter from agro ecological zones. Pearson's correlation analysis was carried out to investigate association patterns among quantitative traits. In order to describe the variation of the set of variables together principal components analysis (PCA)  [28]  was carried out using packages "FactoMineR"  [29]  and Factoextra  [30]  in R software version 3. 5. 1  [31]. Moreover, hierarchical clustering on principal component (HCPC)  [32]  analysis and linear discriminant analysis (LDA)  [33]  were used to define hierarchical typologies of fonio accessions and to describe phenotypic groups obtained.
Acknowledgments: The authors wish to thank  MoBreed program  for the financial support. We are thankful to all farmers and agriculture extension services in Benin,  Burkina Faso ,  Guinea, Mali , and Niger. We also thank  Dèdéou Tchopkonhoue ,  Djamilou Ibrahim ,  Doumbia Zan Ibrahima ,  Diarra Cheik , and  Habou Kano  for assistance during the survey, field activities and data analysis.
The final library was denatured with 0. 2 N NaOH, diluted to 7 pM, spiked with 10% PhiX control DNA (Illumina, San Diego, USA) and subsequently sequenced using 2 x 250 cycles on the Illumina MiSeq sequencer. Sequences were processed using the DADA2 package, following the DADA2 standard operation protocol  [41]. Sequences were classified using RDp version 14  [42]  and the resulting sequence and taxonomy table were imported in to the Phyloseq package v1. 18. 1  [43]  to calculate alpha and beta diversity and plotting of taxonomic profiles as described previously  [44]. Fecal samples collected at d 36. 5 were used for SCFA's analysis and calprotectin measurements. To 1 g of sample, 5 mL 10% formic acid solution with 1 mg/mL 2-ethylbutyric acid as internal standard was added, vortexed and centrifuged at 1,200 g for 5 min.
Subsequently, secondary antibodies were applied at room temperature: for PCNA a sHRP-conjugated goat anti-mouse antibody (1:5,000 in Tris buffer, Dakocytomation, Glostrup, Denmark) and for caspase-3, a sHRP-conjugated goat anti-rabbit antibody (1:1,000 in Tris Buffer, Dakocytomation, Glostrup, Denmark) was applied. Detection of a positive immunoreaction was performed using a chemiluminescence system (SuperSignal West Femto Maximum Sensitivity Substrate, Thermo Scientific, Rockford, Illinois, USA). Protein band intensities were quantified using densitometry (GeneSnap and GeneTools software, Syngene, Cambridge, UK). A normalized optical density (OD) was obtained by dividing the protein density by the density of the loading control β-actin (Sigma-Aldrich, Steinheim, Germany).
The obtained cDNA was diluted 10 times with molecular grade water and a control PCR using 2μL cDNA was performed to verify the reverse-transcription reaction. Primers (Table  2 ) used for genes in the study were designed with Primer3Plus. The repeats, the secondary structure and single nucleotide polymorphism in the target sequence were checked with RepeatMarker, mfold and dbSNP, respectively. All these primer sequences were gene isoform specific as they were designed based on certain exon-exon boundaries of published pig gene sequences corresponding to the accession number. Primers were then purchased from IDT (Integrated DNA Technologies, Leuven, Belgium). The RT-qPCR was carried out on the CFX96 Touch Real-Time PCR Detection System (Bio-Rad Laboratories, Inc. ). Briefly, 2μL cDNA template, 5 μL 2X KAPA SYBR FAST qPCR Kit Master Mix (Kapa Biosystems, Inc.
, Wilmington, USA), 2 μL molecular grade water, 0. 5 μL forward primer and 0. 5 μL reverse primer (5 μM each) were added to a total volume of 10 μL. The amplification conditions were as follows: 1) enzyme activation and initial denaturation (95˚C for 3 min); 2) denaturation (95˚C for 20 s) and annealing/extension and data acquisition (annealing temperature depending on primer for 40 s) repeated 40 cycles; and 3) dissociation (melt curve analysis from 70 to 90˚C with 0. 5˚C increment every 5 s). The primers used in this study were first optimized by gradient quantitative real-time PCR. A 5-fold dilution series (5 points, from 1 to 625 times dilution) of cDNA as a standard curve was included at 3 gradient temperatures to determine PCR amplification efficiency and specificity. The standard curve was also included in each run to determine PCR efficiency.
In this study, PCR amplification efficiencies were consistently between 90 and 110%. Gene-specific amplification was verified by agarose gel electrophoresis and melting curve analysis. Efficiency was used to convert the Cq value into raw data with the highest expressed samples (lowest Cq value) as a calibrator for the normalization of raw data. The relative expression was expressed as a ratio of the target gene to the geometric mean of 3 stable expressed reference genes (ACTB, TOP2B and TBP)  [45, 49].
Statistical analysis The data from the piglets that remained at the farm were used for the analysis of performance parameters. For the fecal samples and the parameters determined using samples of piglets euthanized at d 15 post-weaning the data were not split up according to the BiW category since only NBW piglets were used. Linear mixed models were fitted to evaluate the effect of treatment, age and BiW (performance data only) on the outcome variables (JMP pro 13. 0). Fixed factors included treatment, age, BiW (performance data only) and the interaction between the different fixed factors. To account for the dependence between the observations on littermates, sow was included as a random factor. For the different measurements of body weight on the same pigs at different ages, piglet nested in sow was added as a random factor.