dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analysis Evaluation of the relative miRNA expression was calculated by the comparative cycle threshold method (2 -ΔΔCt )  [33]  and the Ct values normalization by the quantile method. The clustering based on expression profiles was carried out using an unsupervised hierarchical clustering, utilizing Pearson's correlation as a distance measure and average linkage as agglomerative algorithm. The statistical analysis of Microarray (SAM) analysis has identified miRNAs with statistically significant changes in expression profile. A FDR corrected p-value <0. 05 was applied to identify statistically significant differences. All differential expression analyses were run in R using the samr package  [34]. Descriptive and inference statistics were carried out with the statistical software STATA version 15 (StatsCorp, Texas, US).
MiRNA expression profiles We performed RT-qPCR data using TaqMan Low-Density Array (TLDA) in CRC and NCT. After normalization and removal of miRNAs that were not expressed in our cohort, miRNAs expression levels were used to perform unsupervised hierarchical clustering analysis, which allowed clear separation of healthy colon mucosa from tumors. Afterwards, the cancer tissues were divided in two subgroups: CRC with mutation in KRAS gene and CRC with wildtype KRAS gene (Figure  1 ). SAM analysis identified five miRNAs differentially expressed between KRAS-mutated CRC and KRAS-wildtype CRC and between KRAS-wildtype CRC and NCT. The RT-qPCR analysis performed on 754 miRNAs has allowed identifying deregulated miRNAs included only in TLDA Card A. Specifically, overexpression of miR-31-5p and downregulation of miR-425-5p were found in KRAS-wildtype CRC compared to NCT.
Acknowledgments All authors would like to thank the  CRS4 HPC group  for IT support and computational infrastructure. This work was supported in part by grants from  Fondazione di Sardegna, Italy  and from  Regione Autonoma della Sardegna , Italy -Anno 2012, Legge Regionale 7 agosto 2007, n. 7: " Promozione della Ricerca Scientifica e dell'Innovazione Tecnologica in Sardegna ". We are grateful to  Prof. Ciriaco Carru , from the  Department of Biomedical Sciences of the University of Sassari , for his suggestions during the planning of the study and for the financial support, granted by  Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR, Italy) -Progetti di Ricerca di Rilevante Interesse Nazionale   -PRIN 2015 (Prot. 20157ATSLF_002 ) and  Consiglio Nazionale delle Ricerche Flagship InterOmics  (cod.
The expression/activation of platelet receptors was determined by flow cytometry (BD LSRFortesa R X20). Unstimulated or stimulated platelets with thrombin (0. 05 U/mL) were used as controls for each experiment. The data obtained were analyzed using Kaluza software R. To examine the expression of platelet receptors by confocal microscopy, washed human platelets were labeled with TLR monoclonal antibodies  (Vancraeyneste et al. , 2016). Specific slides (wells 6. 7 mm; Thermo Scientific, France) were used in this experiment and the coverslips were examined by confocal microscopy (Zeiss LSM710, Zeiss Airyscan SR mode x6311. 4).
In parallel, the activation of integrin α IIb β 3 was assessed in thrombin-stimulated platelets pretreated with chitin at a concentration of 20 µg/mL (Supplementary Data). A significant decrease in integrin α IIb β 3 activation was observed in thrombin-stimulated platelets when  compared to those untreated with chitin. These data corroborate the aggregation assay showing that chitin pre-treatment reduces platelet aggregation. Using PCR, we also investigated the expression of different TLRs that are known to sense many PAMP molecules, including chitin, promoting the host defense against pathogens (Figure  4 ). Western blot was then performed to confirm the expression of these receptors. A histone marker was used to exclude the presence of leukocytes in the platelet isolate. The human macrophage-differentiated THP-1 cell line was employed as a control.
albicans cells  (Mora-Montes et al. , 2011). In a dextran sulfate sodium-induced colitis model, oral administration of fungal chitin reduced the inflammatory parameters and leukocyte infiltration into the gut mucosa and increased IL-10 production via stimulation of NOD-2 and TLR8  (Vancraeyneste et al. , 2016). In the present study, a large panel of TLRs receptors were analyzed in platelets by RT-q-PCR (Supplementary Data). In contrast to macrophages differentiated from Thp1 cells pre-treated with chitin, which showed high mRNA transcript and protein expression of TLR2 (data not shown), we did not observe any increase in TLR2 mRNA transcripts or protein expression in thrombin-activated platelets pre-treated with chitin. TLR4 was expressed independently of chitin treatment. Of note, treatment of inactivated platelets with chitin did not show any significant increase in TLR8 mRNA levels, while TLR8 transcript levels were significantly increased in thrombin-activated platelets pretreated with chitin.
This is acceptable only if the distance between the precipitates is large in comparison to the diffusion length. For a one-size distribution of ellipsoidal precipitates, g β is simply given by g β = N β • 4 3 πa 3 1 1 -e 2 12 1 -e 2 31. (18) For spherical precipitates, e 12 and e 31 are equal to zero. Table  1  presents the parameters describing the system in which the precipitates are evolving. For the DICTRA simulation, the matrix is an FCC (the name of the phase in the DICTRA software application). A1 phase having an external radius matching the number density of the approximate finite size model. All calculations were performed with DICTRA version 2016a using the TCAL5  [13]  and MOBAL1  [14]  databases. In addition, we require some equilibrium parameters, which are shown in Table  2. The equilibrium data were obtained by using Thermo-Calc  [12]  and the TCAL5  [13]  database.
Discussion The mixed-mode model, which was originally developed for the growth of one particle in an infinite matrix, has been adapted for the growth and dissolution in a finite system, making the model suitable for comparison with a software application like DICTRA. The agreement with the DICTRA simulations for cases where the interfacial mobility is very high is such that one can acknowledge the accuracy of the time discretization procedure described above. Although some authors stated that the reverse-growth approximation is not the best method to calculate the dissolution rate of a precipitate, our results show that the agreement between our reversed-growth model and the DICTRA fully transient solution is in fact excellent, and could only be improved if the analytical procedure accounted for the transient term in the mass conservation equation.
For these time courses, cortical fluorescence intensities were expressed relative to the mean cortical fluorescence intensity of the protein in question within its domain at maintenance phase. Image analysis -PAR-3 cluster quantification PAR-3 cluster tracking was performed in Python using the trackpy package (https://github. com/soft-matter/trackpy). Custom Python code developed for the analysis is available at https://github. com/lhcgeneva/SPT. Briefly, a Crocker-Grier algorithm detects local intensity peaks, which are then fit to a Gaussian point spread function with the detection threshold adjusted empirically for imaging conditions. The sum of integrated intensities across all clusters was calculated for each time point and normalized to area imaged.
ACKNOWLEDGMENTS The authors thank  Franck Pichaud ,  James Briscoe , and members of the  Goehring Lab  for critical comments and  Carrie Cowan  for sharing unpublished observations. Strains and/or reagents were graciously provided by  Mike Boxem ,  Dan Dickinson ,  Andy Golden ,  Monica Gotta ,  Ken Kemphues , and  Geraldine Seydoux. This work was supported by the  Francis Crick Institute  (N. W. G. ), which receives its core funding from  Cancer Research UK  ( FC001086 ), the  UK Medical Research Council  ( FC001086 ), the  Wellcome Trust  ( FC001086 ), and the  EU   Horizon 2020 Research and Innovation Program  under the  Marie Skodowska-Curie  grant agreement  675407. N. W. G. is a member of the  GENiE network , supported by  COST Action BM1408  and  EMBO. Some strains were provided by the  Caenorhabditis Genome Center (CGC) , which is funded by  NIH Office of Research Infrastructure Programs  ( P40 OD010440 ).
sc/ N/A Prism Graphpad Software, Inc. 7. 0c Metamorph Molecular Devices Trackpy http://soft-matter. github. io/ 0. 3. 1 trackpy/v0. 4. 1/ Python https://www. python. org/ 3. 5. 4 Other PolybeadÒ Microspheres 20. 00mm Polysciences 18329-5 PolybeadÒ Microspheres 0. 10 mm Polysciences 00876-15 CONTACT FOR REAGENT AND RESOURCE SHARING Current Biology 29, 1911-1923. e1-e5, June 17, 2019 e2 B C. elegans -Strains and maintenance B C. elegans -Transgenic animals B Bacterial strains.
Understanding the dynamics of the magmatic evolution of the interior of the Moon requires accurate knowledge of the viscosity (η) of lunar magmas at high pressure (P) and high temperature (T) conditions. Although the viscosities of terrestrial magmas are relatively well-documented, and their relation to magma composition well-studied, the viscosities of lunar titano-silicate melts are not well-known. Here, we present an experimentally measured viscosity dataset for three end member compositions, characterized by a wide range of titanium contents, at lunar-relevant pressuretemperature range of ∼1. 1-2. 4 GPa and 1830-2090 K. In situ viscometry using the falling sphere technique shows that the viscosity of lunar melts varies between ∼0. 13 and 0. 87 Pa-s depending on temperature, pressure and composition.
Heating to the final temperature was performed very rapidly at a rate of 100 W/min to ensure full and rapid melting of the sample above the liquidus. At different stages of the experiments, synchrotron X-ray diffraction patterns were systematically collected for both sample and calibrants. All 2D diffraction images were treated and integrated using the Fit2D data analysis software  (Hammersley et al. , 1996). Sample diffraction patterns were used to assess the physical state of the sample (Figure  2 ). Note that the diffuse scattering from the liquid that is observed in diffraction patterns (Figure  2  middle) is not readily suitable for structural investigations of the melt structure because (i) incident X-ray energy was optimized for radiography contrast instead of diffraction quality and (ii) measured intensities were not corrected for the response of the Sollers slit which is non-linear (see  Morard et al.
RESULTS We performed a total of seven successful runs covering the temperature range between 1830 and 2090 K and pressure range from 1. 1 to 2. 4 GPa (Figure  3  and Table  2 ). Time-lapsed radiographic images of a typical successful run are shown in Figure  4 , with a falling rhenium sphere measured at 2. 4 GPa and 1906 K in a molten black glass sample (sample B2, also shown in Figure  2 ). The corresponding time versus falling distance profile (Figure  4 ) is constructed from the location of the top and bottom points of the sphere, tracked on each individual frame using the Metavue R image software. The time-falling distance FIGURE 3 | Pressure-temperature conditions of the in situ viscosity measurements for the green (circles), orange (triangles) and black (squares) glasses, compared with experimentally determined liquidi for the green, orange and black glasses compositions  (Wagner and Grove, 1997; Elkins-Tanton et al.
The best fit parameters are E a = 201 ± 26 kJ/mol -logη 0,T = -5. 8 ± 0. 7 Pas and E a = 106 ± 46 kJ/mol -logη 0,T = -4. 1 ± 1. 5 Pa-s for the green and black glass, respectively. For the orange glass, we consider the activation energy E a to range between the two above values considering its intermediate composition. These activation energies suffer from significant uncertainties because of the limited dataset; however, they are in agreement with activation energies for viscous flow determined experimentally at high-temperature (T > 1600 K) and ambient pressure for a variety of silicate melts  (Mysen and Richet, 2005). For example,  Liebske et al. (2005)  measured an activation energy E a = 197 kJ/mol for a peridotite liquid. For Ti-bearing ferrobasaltic melts,  Chevrel et al. (2014)  reported E a = 179 kJ/mol for a 1.
In contrast, another study found a negative association between boldness and female fecundity in mosquitofish (Gambusia affinis)  [18] , indicating that negative consequences of being bold exist in this species, it is however important to note that lower fecundity may not necessarily translate into reduced reproductive success. Similarly, some studies suggest a negative effect of boldness on survival (reviewed in  [6] ). In addition to these positive and negative associations a number of studies found no association between boldness and fitness (e. g. [9, 10] ). Thus, to date we have no overall consensus regarding the relationship between boldness and fitness. More data are needed to make generalizations about non-neutrality, and direction of the effect. Here, I used guppies to examine the association between boldness and male reproductive success.
Results Of the 70 males for which complete data on boldness and colouration was collected, 30 (43%) successfully sired offspring, and the mean number of offspring sired by a father was 5. 9. The distribution of boldness scores across aquaria is represented in Additional file 1: Figure  S1. The clutches of 18 females were sired by a single male, 16 females had clutches which paternity was assigned to two males, and two females had clutches assigned to three males. Boldness, orange area and body size did not predict success or failure of a male to reproduce (boldness: z 7,69 = -0. 82, p = 0. 41; orange area: z 7,69 = 0. 76, p = 0. 45; body size: z 7,69 = -0. 01, p = 0. 99). There was a significant effect of boldness on the number of offspring sired: bolder males sired more offspring (z 7,71 = -0.
A similar effect has been previously reported in zebra fish, where eggs sired by bold males had improved viability  [15]. This could be the case here, as I measured male reproductive success as the number of offspring after birth. Thus, "bigger clutch" ascribed to a female may be an effect of better juvenile survival, rather than of bigger clutch produced. Discrimination between the alternatives discussed above will require further research. Irrespective of underlying mechanism, my data show that male boldness is associated with higher fitness. This highlights the need for an explanation for the presence of variation in personalities. The experiment here was conducted in the absence of predators. Under predation pressure there could potentially be a boldness-related trade-off between individual whole-life reproductive success and survival, since bold fish behave in a more risky way and are thus expected to be under increased risk of predation.
Thus, this approach enabled me to minimise potential differences in mating motivation and investment in reproduction for both sexes. After 1 week of mating, males were removed, the tips of their tail fins were taken for DNA analysis, and they were photographed on their left side under anaesthesia (MS-222). Females were kept in breeding chambers until parturition, after which their tail-fin tips were also taken. Tail-fin tips were sampled from all male and female F1 guppies. All fin samples were stored in 95% ethanol until DNA extraction. All tests and measurements were carried out blindly with respect to the results of the other analyses. Body area (excluding tail fin) and the area of carotenoid (orange, red, and yellow) spots of all males from the parental generation were measured from photographs using Image J software  [51].
Immunohistochemistry Three-mm-thick sections of formalin-fixed and paraffinembedded (FFPE) FL lymph node tissues were stained with an anti-NKP46 antibody (kindly gift by Pr Eric Vivier, Innate Pharma, Marseille, France). Whole slides were digitalized using Pannoramic 250 Flash II digital microscopes (3DHISTECH, Hungary) and read by a pathologist at the IUCT (Toulouse, France). IHC staining was evaluated and percent of NK cells was quantified by automated method using Tissue studio image analysis software (Definiens, Munich, Germany). mAbs Trastuzumab (TTZ, Herceptin), rituximab (RTX, Mabthera) and Obinutuzumab (GA101) were provided by Genentech (San Francisco, USA), Roche (Boulogne-Billancourt, France) and Roche (Zurich, Switzerland), respectively.
Gene Expression Analysis The GEO Datasets (29) were sourced for FL gene expression profiles obtained with the Affymetrix HG U133 plus 2. 0 microarray platform. We downloaded raw data from studies GSE53820 (30), GSE55267  (31) , GSE65135 (32), GSE16024 (unpublished), GSE21554  (33) , and GSE38816  (34)  and normalized these together by the method RMA. Then, these transcriptomes were collapsed to around 21000 HUGO protein-encoding gene symbols. The sample enrichment scores (SES) were computed by Auto-Compare-SES (https://sites. google. com/site/fredsoftwares/products/autocompare_ses) with normalized settings (35). NK and B cell SES signatures were from CIBERSORT  (33, 36)  based on the expression of genes listed in Supplementary Figure  1. The cytolytic T cell gene signature was defined based on the expression of 8 genes: GZMA, PRFN, GZMB, GZMK, GZMM, GZMH, TRAIL, and IFNG.
Functional NK Cells Infiltrate FL Lymph Nodes We first analyzed a large cohort (n = 169) of public available transcriptome  (29) (30) (31) (32) (33) (34)  datasets of FL biopsies by data mining. The composition of tumor infiltrating leucocytes was deconvolved as depicted (35) and SES of B and NK cells, corresponding to a transcriptomic signature of 79 genes, respectively (Supplementary Figure  1 ) was determined. As shown in Figure  1A  and in line with the FL cell of origin, "B cell" SES is predominant in all samples (mean SES for "B cells": 65. 4; range: 28. 1-91. 3). Interestingly, we find that "NK cell" SES, with a mean of 9. 05 (range: 0. 01-33. 03), correlates with a cytolytic index (Figure  1B ). Next, we measured NK cell percent by flow cytometry on a series of fresh human FL biopsies, normal tonsil and reactive lymph nodes (see Supplementary Figure  2 , Supplementary Tables 1, 2 for sample characteristics), and show that number of infiltrated NK cells increases in both FL (mean: 1.
11, range: 0. 2-3. 35) and reactive lymph nodes (mean: 1. 67, range: 0. 6-3. 4) compared to normal tonsil (mean: 0. 584, range: 0. 2-2. 5) (Figure  1C ). Immunohistochemistry of NKP46 on FFPE FL lymph nodes reveals that NK cells mainly localize at the interfollicular spaces (Figure  1D , left panel). However, we observe a heterogeneity among FL patients with patients presenting a strong NKP46 labeling (Figures  1Di, ii ) and others presenting a weak labeling (Figures  1Diii, iv ). Quantification of NK cell percent on this FL cohort validates results obtained by flow cytometry (Figure  1D , right panel). We wondered whether the presence of NK in FL biopsies could be correlated with patient survival. Thus, we analyzed by data mining (n = 169) public available transcriptome datasets of FL biopsies on their content of NK and determined the PFS.
ACKNOWLEDGMENTS We thank all members of J-JF's team and  Christine Jean  ( CRCT, Toulouse, France ) for fruitful discussion,  Laetitia Ligat  ( pôle technologique, CRCT, Toulouse ) for her help on confocal microscopy,  Pr Eric Vivier  ( Innate Pharma, Marseille, France ) for providing anti-NKP46 antibody, and the patients and their family for contributing their samples.
FUNDING This work was funded by institutional grants from  INSERM ,  Université Paul Sabatier  and  CNRS, Laboratoire d'Excellence TOUCAN  (contract  ANR11-LABEX ),  Institut Hospitalo-Universitaire Programme CAPTOR  ( ANR-11-PHUC-0001 ), and  Roche  ( R16067BB ). CR receives a grant from  ITMO Cancer dans le cadre du Plan Cancer   2014-2019. PG was supported by the  CALYM Carnot Institute.
After dehydration with acetonitrile, the proteins were cleaved in gel using 12. 5 ng/µl of modified porcine trypsin (Promega) in 25 mM NH 4 HCO 3 at 37°C overnight. The tryptic peptides were extracted twice, using 0. 4% CF 3 CO 2 H in CH 3 CN/H 2 O (60/40) for the first extraction and 100% CH 3 CN for the second extraction. The volumes were then reduced to 5 µl by speed vacuuming to eliminate acetonitrile and to concentrate the peptides. Samples were analyzed using an Agilent 1200 series HPLC-Chip/MS system (Agilent Technologies) coupled to an HCT Plus ion trap mass spectrometer (Bruker Daltonics), as previously described  (13). MS/MS data sets were processed using the Mascot search engine (Matrix Science)  (13). Spectra were searched with a mass tolerance of 0. 5 Da for MS and MS/MS data, allowing for a maximum of one missed cleavage with trypsin and with carbamidomethylation of cysteines, oxidation of methionines, acetylation of protein N-terminal, phosphorylation of serines, threonines and tyrosines specified as variable modifications.
Chloroquine efflux assay Chloroquine efflux kinetics were determined as described  (16). Briefly, magnet purified P. falciparum-infected erythrocytes at the trophozoite stage were resuspended in transport buffer (see above) at a hematocrit of approximately 25,000 cells µl -1. [ 3 H]-chloroquine was added to a final concentration of 100 nM and the cells were incubated at 37 o C for 15 minutes. Cells were then washed twice in ice-cold transport buffer (pH adjusted to 7. 3 at 4 o C) before they were resuspended in prewarmed transport buffer at a hematocrit of 9,000 cells µl -1. 150 µl aliquots were withdrawn at the time points indicated and the amount of extracellular and intracellular [ 3 H]-chloroquine was determined as described above. The initial efflux rate was determined by plotting the amount of intracellular chloroquine as a function of time and fitting a single, three parameter exponential decay equation to the data points.
The samples were then washed again 3 times and kept over-night in PBS at 4ºC until they were imaged in a perfusion chamber using an LSM 510 confocal microscope (Zeiss). The samples were excited using a 488 nm Argon ion laser and the emission was detected using a 505-550 nm band pass filter. The objective used was a C-Apochromat with 63 x magnification. The images were acquired using the LSM imaging software and processed with the FIJI program.
Statistics and reproducibility Statistical analyses were performed, using the Sigma Plot (v. 13, Systat) software. Statistical significance was determined using the Holm-Sidak one way ANOVA test, the Student's t-test or the F-test, where appropriate. The number of independent biological replicates is indicated in the main text and/or the figure legends, and in most cases corresponds to the number of individual date points depicted in the graph. If independent data points are averaged, then the mean ± standard error is shown. Independent biological replicates are defined as independent infections using blood from different donors or independent experiments using oocytes from a different frog. Table  1. Kinetic parameters for chloroquine transport of PfCRT Dd2 and Ser-33 mutants. Best-fit values of kinetic parameters were obtained from the kinetics of chloroquine uptake depicted in Fig.