dataesr/scientific-paragraphs-categorization huggingface dataset:
After washing with PBS-BSA (0. 5% BSA), samples were acquired at either FACSCanto II or FACSFortessa (BD Biosciences, San Jose CA, USA) coupled to computers with Diva software for flow cytometry analysis. Populations of interest were delimited by size and granularity (Forward Scatter × Side Scatter), and 50. 000 or 100. 000 events were acquired for subsequent analysis using FlowJo software. Fluorescent-dye-conjugated monoclonal antibodies (mAbs) were anti-mouse CD8α, 60-0081-U100, Pe-Cy7 (53-6. 7); antimouse CD45 103108, FITC (30-F11); anti-mouse CD8b, 37.
Isolation of fecal content and microbiota DNA from feces Fecal DNA was extracted from fresh mouse fecal samples using the QIAamp DNA Stool Mini Kit (QIAGEN, Hilden, Germany). DNA sequencing of microbiota was performed in the DNA purified from feces was amplified at the V3-V4 hypervariable region of RNA ribosomal 16S and sequenced using the Illumina-MiSeq platform (Illumina, San Diego, CA), which provided single-end reads with 150 nt in length. Downstream analysis was performed by running the QIIME (Quantitative Insights into Microbial Ecology) pipeline. Briefly, sequence reads that presented Phred quality score smaller than 20 were removed. We normalize each library relative to the smaller sample, choosing randomly until it matches its total number of readings. Afterward, representative sequences were grouped by Uclust into Operational Taxonomic Units by 97% similarity and taxonomy assigned with Pynast against the Green genes database.
Human subjects Jejunum biopsy samples were obtained from 60 subjects with severe obesity who met the recruitment criteria for bariatric surgery 79. As part of usual patient care, the BARICAN cohort is recruited and followed up at the Pitié-Salpêtrière Hospital Nutrition Department (Paris, France). In agreement with ethical regulation, patients provided informed consent and are part of several studies registered on https://clinicaltrials. gov (P050318 Les Comités de Protection des Personnes (CPP) approval: 24 November 2006, NCT01655017, NCT01454232)78. This cohort also got approval by CNIL (Commission Nationale de l'Informatique et des Libertés; No. 1222666) and the French Ministry of Research. All patients met standard bariatric surgery indications and are monitored according to national and international guidelines.
Patients were not involved in this work's design, conduct, reporting, or dissemination plans. Before bariatric surgery, height and weight were measured by standard procedures. Blood samples were collected after 12 hours of overnight fasting 79. The clinical data of these individuals are described in S1. Insulin resistance was estimated by calculating HOMA-IR as (glucose [nmol/l]*insulin [mU/ml]/22. 5) using fasting values80. T2D was diagnosed in accordance with American Diabetes Association (ADA)definition  62. Serum samples were collected at the fasting state for IgE evaluation. After clinical and biological evaluation, patients were all operated on in the visceral surgery department of Pitié-Salpêtrière hospital in Paris.
FUNDING This work was supported by research grants from  Fundação de Apoio à Pesquisa do Estado de Minas Gerais -FAPEMIG  (( APQ 00704-14 ,  RED 00140-16 ) and  Pro-Reitoria de Pesquisa (PRPq) UFMG. LT, VMD, MAO, and LMT are recipients of scholarships, and  TUM , MR, and  AMCF  are fellowships from  Conselho Nacional.
1 mm, 5 µm, Supelco, Bellefonte, PA) and a 5500 QTRAP mass spectrometer (SCIEX, Framingham, MA) was used. PC and PE containing esterified ARA or DHA chains were analyzed by scanning precursor ions of the m/z 303 or of the m/z 327 product anion, respectively. Results were analyzed using MultiQuant software (SCIEX) and all detected ARA and DHA containing PC and PE results are reported as the ratio between the integrated area of each analyte and the integrated area of the corresponding internal standard (IS) for PC class (PC In order to distinguish vinyl ether (P = plasmalogen) from 1-O-alkyl (O = ether) linkages at the sn-1 position of PC and PE species, acid labile plasmalogens were hydrolyzed by exposure to 12N HCl fumes  [39]. This was achieved by drying down the placenta total lipid extract under a stream of nitrogen followed by exposure to hydrochloric acid fumes for 1 h.
Statistical analyses All statistical analyses were performed using GraphPad Prism version 9. 01. Results are expressed as mean ± SD for each sample type; maternal vein (MV), placenta, umbilical vein (UV) and artery (UA). Chi-square test was used to compare qualitative data in obese and control groups. Data distribution was assessed by the Shapiro-Wilk normality test. All lipid variables were compared between two independent groups, control vs obese groups and separated by fetal sex, in each sample. We applied the Benjamini-Hochberg false discovery rate adjustment to account for multiple testing. All tests were two-sided. A significance threshold set at q ≤ 0. 05 was used for the targeted lipidomic analysis  [40]. Correlation analysis with spearman test was performed to assess correlations between maternal obesity and ether and plasmalogen PC and PE species in placentas and in umbilical cord.
Acknowledgements The authors thank  Dr. Robert Murphy  who was the chief of the  Mass Spectrometry Lipidomics Core Facility  at the  University of Colorado Anschutz Medical Campus, Aurora, Colorado  where all the targeted lipidomic analyses were performed in plasma and placental tissue. We also thank  Anita Kramer  and  Kathryn Erickson  who helped for collection and processing blood and placenta samples. We are grateful to staff at the  Clinical and Translational Research Center (CTRC) at the University of Colorado Hospital  for collection of placental tissue.
Principal component analysis of CMB heat flux We use a principal component analysis (PCA) to obtain the dominant heat flux patterns at the bottom of the mantle in the different models. PCA is a data analysis tool that can be applied to a dataset comprising several observations, each observation depending on several variables. It is used to express the dataset in a new orthonormal basis in order to limit the number of variables needed to explain the data. This is done by computing new variables (called principal components), which are combinations of the initial variables. A full mathematical description of PCA theory is given by  Abdi and Williams (2010) ; see also  Pais et al. (2015)  for an application to core flows and details of the method. Considering a data set containing I observations described by J variables, the PCA consists in a singular value decomposition of the I × J data matrix D as D = WSP, (3) where W, S and P have respective dimensions I × K, K × K and K × J, with K = min(I, J) the rank of the data matrix.
Sections were washed in PBS 1 × 2 times for 10 min, incubated 30 s with DAPI, and washed once in PBS for 10 min and mounted with Aqueous Mounting Medium PermaFluor™. For the morphometric analysis, muscle sections were scanned using a NanoZoomer (Hamamatsu Photonics) with a 20X objective. Image J free software was used to analyze and quantify the pictures for each entire area.
Protein isolation and western blotting analysis Frozen liver or muscle samples were homogenized using an Ultra Turax homogenizer. Protein levels were assessed by Western blotting. Total proteins were measured using the Bio-Rad protein assay according to the manufacturer's instructions. Signals were revealed using a ClarityTM Western ECL Substrate Kit, and proteins were visualized by enhanced chemiluminescence using the ChemiDoc Touch Imaging System and quantified with Image Lab. Touch Software (version 5. 2. 1).
In DIO mice, FuFA-F2 had no effect on plasma CMPF concentrations 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) is one of the major endogenous metabolites of furan fatty acids and omega 3 fatty acids  [33, 34]. Interestingly, Prentice et al. [35]  showed that administration of CMPF to mice before or after high-fat diet feeding improved insulin sensitivity, increased beta-oxidation and reduced hepatic steatosis. In order to verify whether the different health benefits of FuFA-F2 supplementation could be related to an increase in CMPF, we measured plasma CMPF concentrations in mice. However, our results showed that FuFA-F2 supplementation did not induce any increase in CMPF in the plasma of mice (Fig. 8 ). These data indicate that the health benefits of FuFA-F2 are not related to an increase in plasma CMPF levels.
This set of data reveals that preventive FuFA-F2 supplementation largely prevents the development of metabolic disorders in mice fed an obesogenic diet (Fig. 9 ). In our previous study, we showed that 3 weeks of oral gavage in C57Bl6 mice with FuFA-F2 at a concentration of 20 mg/day/kl was sufficient to induce an increase in muscle mass in these animals  [26]. However, in this work we have privileged a nutritional approach and we have chosen to test two different higher doses of FuFA-F2 (40 mg and 110 mg/day/kg of body weight) as they are integrated in the food matrix. The use of these two different doses of FuFA-F2 provided interesting data. Thus, whatever the dose, identical results were obtained on resting energy expenditure, glucose tolerance and insulin sensitivity. On the other hand, we observed dose-dependent effects on fat mass, lean mass, quadriceps weight and reduction of hepatic steatosis.
Acknowledgements We thank  Mélanie Macart  from the animal staff for daily animal care. We thank  Pierre Delobel  for these helpful suggestions for morphometric analysis of muscle sections. The authors also wish to thank the  Metamus DMeM facility  (https://doi. org/10. 15454/WYR2-8706 ),which belongs to the Montpellier animal facilities network ( RAM, Biocampus)  for technical support and expertise for metabolism phenotyping, and Metamontp platform supported by the  European fund for the regional development of Occitanie (FEDER). The authors also thank the " Réseau d′ Histologie Expérimentale de Montpellier " (RHEM) histology facility for processing our liver samples and  Genotoul Anexplo  for biochemical analysis of blood samples.
Funding This work was supported by the  French National Research Institute for Agriculture, Food and Environment (INRAE) , by the  French Lipid Nutrition Group  and by the by the  Key Initiative Food & Health of MUSE (Montpellier University of Excellence ). Laetitia Dore was funded by  Agence R´egionale de Sant´e Occitanie. CRediT authorship contribution statement L. D. , E. D. , B. B. , J. C. , L. V. , S. L. , L. P. , K. L. , C. B-G. , and F. C acquisition of data. E. D. , S. G. , C. C. , A. S. , F. C. , and C. F-C. analysis and interpretation of data. C. F-C. and F. C. conception and design, wrote the paper. All the authors have read and approved the final version of this manuscript.
Development of the food photography atlas We developed the FP atlas for cooked food items or complete dishes according to the guidelines proposed by Nelson and Haraldsdottir  [23, 24]. Food choice. We selected eleven traditional food items/dishes from the database of a previous food consumption survey carried out in Ouagadougou (INSTAPA project, unpublished data, 2009): five cereal-based staple food items (stiff corn porridge, fermented millet porridge, cowpea with rice, rice, and spaghetti), one leafy vegetable dish, three sauces (groundnut paste sauce, vegetable sauce, dried okra sauce), and two standalone food items (pieces of meat and fish). We chose these food items on the basis of the following criteria: their high consumption frequency or the difficulty of using other methods to estimate the consumed portions.
As meat and fish are rarely consumed by 6-11-month-old children, we did not include them in the atlas for this age group. Portion size determination-Data collection. To roughly estimate the portion sizes to include in the FP atlas, we determined the most frequent portion sizes for the groups targeted by this study (6-11-month and 12-23-month-old children and women of childbearing age) through a preliminary 24-hour portion recall survey using SRs. The aim was to quantify portions in at least ten people for each food item and for each group. We carried out this preliminary survey in 130 households visited at random and that included women of childbearing age, 6-11-month children, or 12-23-month-old children in January 2020. Half of participants in this survey lived in a central area of Ouagadougou (with urban infrastructure i.
Data collection and analysis We collected data on digital tablets using KoboCollect™-generated Excel forms to allow their quick and correct transfer to the KoboToolbox™ platform. We performed all statistical analyses with the R software, version 4. 0. 5. We calculated the means and standard deviations (SD) of the amounts of food consumed. As data most often did not follow the normal distribution, we used the Spearman's test to assess correlations between the estimation methods and the reference method. We calculated the mean of the differences between estimated and weighed portions and the means of the absolute values of these differences (in grams) and corresponding relative errors (based on the reference values). We used Lin's coefficients to assess the agreement between each estimation method and the reference method  [26, 27].
Depending on the food items, the mean differences ranged from an underestimation of 40g to an overestimation of 19g  [16, 25, 34]. Some studies recorded lower errors (from -35 to +40%) with an FP atlas  [16, 25, [40] [41] [42] [43] , but their data were not expressed in absolute values. In our study, errors in the estimated portion sizes increased with the average portion size consumed and were smaller for 6-11-month-old than for 12-23-month-old children. Few studies reported the validation of a FP atlas developed for <2-year-old children. Three studies in children and adolescents with recalls immediately after consumption found mean differences between -40 and 49g (with errors between -24 to +20%), depending on the food item  [19, 21, 44]. Using an age-appropriate FP atlas, Foster et al. concluded that parents underestimate their pre-school children's served portions by 5%, on average, and overestimated their consumed portions by 7% (with agreement limits from -75 to +357%)  [37].
Statistical Analysis Differences between years are not shown because there were no significant differences between them. All samples were analyzed in triplicate. The results are expressed as the means of the triplicate measurements. The values were statistically evaluated by analysis of variance (ANOVA), and further, Tukey's honestly significant difference tests were performed for mean comparisons (Minitab release 14 statistical software, 2003; Minitab Inc. , State College, PA, USA). Differences are considered significant at p ≤ 0. 05  [49].
This could ultimately co-enrich eukaryotic cells in these metals and explain the high Co, Ni, Zn, and Mn concentrations found in the Francevillian Group fossilized structures, which further points to their possible eukaryotic affinity. Although Ag analyses were not made on bulk host rocks and microbial mat structures, LA-ICP-MS data show that Ag is enriched in the Francevillian Group fossilized structures, with concentrations ≥10 µg/g, compared to early diagenetic pyrite unrelated to these structures, with concentrations <10 µg/g (Fig. 4 ; Table  S1 ). The same applies to other Paleoproterozoic pyrite with Ag concentrations averaging 3 µg/g (ranges between 1 and 7 µg/g;  Large et al. , 2014). Considering that diagenetic pyrite is an authigenic mineral phase prone to record environmental geochemical conditions, Ag concentrations found in these pyrite phases likely reflect the aqueous Ag concentration in seawater (for pyrite beds) and sediment pore-waters (for concretions).
The Francevillian Group organisms: evolutionary response to the GOE? Based on the high Zn, Co, Ni, and Mn demand of eukaryotes and preferential uptake of light Zn isotopes, our dataset provides compelling geochemical evidence to suggest both a biogenic and eukaryotic affinity for the c. 2. 1 Gyr old Francevillian Group fossilized structures. If correct, this would suggest that eukaryotes already evolved during the latter part of the GOE. This is consistent with earlier suggestions based on molecular clocks  (Gold et al. , 2017; Strassert et al. , 2021)  that eukaryotes evolved at least 400 Myr earlier than indicated by paleontological and biomarker records (Fig. 6 ). Our findings suggest that complex life forms might have rapidly adapted to the appearance of atmospheric oxygen with the emergence of oxygen-dependent and energetically more efficient eukaryotic metabolism, thus adding to the growing evidence that environmental change, specifically oxygenation of Earth's surface environments, was a major driver of biological evolution.
Acknowledgements FOO and RS acknowledge financial support from the  University of Tübingen  and the  German Research Foundation  ( DFG Grant   SCHO1071/11-1 ). FOO and MBA are thankful for support from the  Natural Environment Research Council  ( NERC grant   NE/V004824/1 ). AH and FOO acknowledge support from  National Research Foundation of South Africa  ( NRF Grant 75892 ) and the  DST-NRF Centre of Excellence for Integrated Mineral and Energy Resource Analysis (CIMERA). Participation by AB was supported by  Discovery and Accelerator Grants  from the  Natural Sciences and Engineering Research Council of Canada (NSERC)  and  ACS PF  grant  624840ND2. SWP acknowledges support from a  Royal Society Wolfson Research Merit Award. We thank  Dr. Ilka Kleinhanns  and  Elmar Reitter  for assistance with Zn isotope measurements.
1 -mm guard cartridge column (Sigma-Aldrich). The mobile phase used was a gradient of solvent A [methanol/water/hexane/ammonium hydroxide, 87. 5:10. 5:1. 5:0. 5 (vol/vol/vol/vol)], solvent B [methanol/hexane/ammonium hydroxide, 87. 5:12:0. 5 (vol/vol/vol)], and solvent C [methanol/water, 9:1 (vol/vol)]. The gradient started at 100% A, decreased linearly to 50% A (50% B) in 17. 5 min and to 0% A (100% B) in 12. 5 min, before being maintained at 100% B for 5 min, changed to 100% C in 3 min, maintained at 100% C for 9 min, and then changed to 100% B in 3 min. The flow rate was 0. 5 ml/min and the injection volume was 80 μl. Data acquisition was carried out in the full scan and positive mode, detecting PC species as [M + H] + ions with the capillary current set at -4000 V. The PC (16:0/18:1) species were characterized by tandem mass spectrometry in the multiple reaction monitoring and negative mode, with a postcolumn addition of acetic acid for [M + CH3CO2]-adduct formation (100 μl/h).
Cell culture The rat hepatocyte cell line BRL-3 A (P9-13, RRID:CVCL_0606) was purchased from the European Collection of Authenticated Cell Cultures (ECACC, Salisbury, United Kingdom). Cells were cultured under standard culture conditions (37 • C, 5% CO 2 ) in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. BRL-3 A cells were incubated in serum-free DMEM in the absence (control cells) or presence of elafibranor (different concentrations), U0126 (different concentrations), GW501516 (10 µM), or GSK0660 (60 µM). BRL-3A cells were transiently transfected with 100 nM siRNA against S100A4 or the control siRNA in Opti-MEM medium (Thermo Fisher, MA, USA) using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) (13. 2 μl per 2. 2-ml well) according to the manufacturer's instructions.
Statistical analysis Results are expressed as the mean ± SEM. Significant differences were assessed by either Student's t-test or one-way and two-way ANOVA, according to the number of groups compared, using the GraphPad Prism program (version 9. 0. 2) (GraphPad Software Inc. , San Diego, CA, USA). When significant variations were found by ANOVA, Tukey's post-hoc test for multiple comparisons was performed only if F achieved a p value < 0. 05. Differences were considered significant at p < 0. 05.
Introduction Thiosemicarbazones (TSCs) are biologically active compounds that have been developed for the treatment of diverse diseases including cancer. 1  Here, especially α-N -heterocyclic TSCs are in the focus of interest, as they are highly potent metal chelators. Consequently, drugs like Triapine (3-AP) or Dp44mT (Scheme 1 ) have been originally developed to exploit the enhanced need of cancer cells for iron (Fe)  2 , 3  with the Fe-containing enzyme ribonucleotide reductase as proposed intracellular target. 4  Based on its promising anticancer activity, Triapine was not only tested in > 35 phase I and II clinical trials  5 -9  but also entered recently a phase III study against cervical or vaginal cancer patients in combination with cisplatin and radiation therapy (study number NCT02466971; www.
clinicaltrials. gov ). 10   (Scheme 1 ). Noteworthy, these two compounds as well as Dp44mT (the predecessor of DpC) and a dimethylated Triapine derivative (Me 2 NNMe 2 ) developed in our laboratory represent a subclass of TSCs characterized by a ∼500-fold higher anticancer activity compared to Triapine in cell culture. 11 , 12  Several studies suggested that this enhanced efficiency could be based on an additional mode-of-action, associated with their ability to chelate also other essential metal ions beside Fe, especially copper (Cu). 13 -15  Indeed, we were recently able to show that the anticancer activity of TSCs is correlated with the stability and, especially, reduction kinetics of their Cu complexes. 16  Moreover, this also influenced the resistance profile of cancer cells, as TSCs with high affinity for Cu form ternary complexes with glutathione (GSH), rendering them substrates for the efflux pump ATP-binding cassette transporter C1 (ABCC1).
ICP -MS/MS An Agilent 8800 ICP-MS/MS instrument (Agilent Technologies, Tokyo, Japan) with oxygen as reaction gas was used to determine the content of the respective elements. The ICP-MS parameters were tuned on a daily based to achieve high sensitivity. The ICP-MS was equipped with a MicroMist nebulizer with a sample uptake rate of ∼0. 25 ml•min -1 and standard nickel cones. The instrument was coupled to an Agilent 1260 Infinity Bio-Inert HPLC system (Agilent Technologies, Waldbronn, Germany). The Agilent MassHunter software package (Workstation Software, Version C. 01. 06, 2019) was used for data evaluation. The instrumental parameters for the ICP-MS measurements are summarized in Table  2.
Funding This work was funded by the  Austrian Science Fund (FWF)  grant number  P31923  (to C. R. K. and P. H. ) and FG3 (to C. R. K. , G. K. , and P. H. ). S. Hager  is a recipient of an  Esprit Fellowship  of the  Austrian Science Fund (FWF , grant  ESP87 ). E. Falcone  is supported by the  French National Research Agency (ANR)  through the  ANR-17-EURE-0016  and  CHAPCOP-ANR-19-CE44-0018  programs.
Remaining stem fragments were fixed in 80% ethanol, then dehydrated using a graded ethanol series. According to the manufacturer's protocol, three individual stem fragments per field area were embedded in Technovit 7100 (Hereaus). Semi-thin sections (5 mm) were obtained with a Leica RM2065 microtome with glass knives. Three spatially separated cross-sections (every 200 mm) were selected for each individual for measurements. Toluidine-Blue O (TBO) coloration (0. 1%, w/v in water) was applied on semi-thin sections to facilitate visual separation between the inner and outer tissues, allowing discrimination of fiber bundles and cell types. Measures were acquired with FIJI free software 1. Cell surface and number of elementary fibers per bundle were further referred to as "inplanta" features.
Six images per fiber batch were measured with the measuring mask Long_fibres_2400dpi_Epson_Bast_uncalib in the FibreShape software (minimum element width: 11 µm). The crosssectional area was calculated from the thickness value of the fiber bundle using a SEM based correction model  (Haag and Müssig, 2016) : Area = d 1. 7256 * 0. 21113, where dthe thickness of the scutched fiber bundle. Strength, Young's modulus, strain, maximum force, and thickness measurements were further refered as "ex-planta" features.