dataesr/scientific-paragraphs-categorization huggingface dataset:
FUNDING This work was supported by grants from  PICT   2015-1954 ,  SECYT 2012-2016 ,  INC-Ministerio de Salud de la Nación Argentina  ( 2015-2017 ) to CLM. FPC, MCR, and SNB were supported by fellowships from  CONICET. NGN was supported by a fellowship from  Ligue Nationale Contre le Cancer AG, EVAR  and CLM are members of the Scientific Career in CONICET. NP is a member of the Technical Assistant Career from  CONICET. The TransImm team is supported by the  SiRIC-Curie Program  (grant  INCa -DGOS-12554 ), the  LabEx DCBIOL  ( ANR-10-IDEX-0001-02   PSL , and  ANR-11-LABX-0043 ), and the  Center of Clinical Investigation  ( CIC IGR-Curie 1428 ).
Background: Osteosarcoma (OS) is the most common type of primary bone cancer affecting children and adolescents. OS has a high propensity to spread meaning the disease is often incurable and fatal. There have been no improvements in survival rates for decades. This highlights an urgent need for the development of novel therapeutic strategies. Here, we report in vitro and in vivo data that demonstrates the role of purinergic signalling, specifically, the B isoform of the purinergic receptor P2RX7 (P2RX7B), in OS progression and metastasis. Methods: TE85 and MNNG-HOS OS cells were transfected with P2RX7B. These cell lines were then characterised and assessed for proliferation, cell adhesion, migration and invasion in vitro. We used these cells to perform both paratibial and tail vein injected mouse studies where the primary tumour, bone and lungs were analysed.
We used RNA-seq to identify responsive pathways relating to P2RX7B. Results: Our data shows that P2RX7B expression confers a survival advantage in TE85 + P2RX7B and MNNG-HOS + P2RX7B human OS cell lines in vitro that is minimised following treatment with A740003, a specific P2RX7 antagonist. P2RX7B expression reduced cell adhesion and P2RX7B activation promoted invasion and migration in vitro, demonstrating a metastatic phenotype. Using an in vivo OS xenograft model, MNNG-HOS + P2RX7B tumours exhibited cancer-associated ectopic bone formation that was abrogated with A740003 treatment. A pro-metastatic phenotype was further demonstrated in vivo as expression of P2RX7B in primary tumour cells increased the propensity of tumour cells to metastasise to the lungs. RNA-seq identified a novel gene axis, FN1/LOX/PDGFB/IGFBP3/BMP4, downregulated in response to A740003 treatment.
Bioinformatics Fastq files were converted to fasta. Trim Galore was used to remove adapter sequences and reads < 20 nucleotides. Trimmed reads were aligned to the human genome (v38) using HISAT2  [39]. Transcripts were download from GENCODE (v28) and Ensembl (v92). Count matrices for transcripts were created using Kallisto  [40]. Differentially expressed (DE) transcripts were determined using the DESeq2  [41]  package in R (v1. 2. 10). DE mRNA according to log 2 fold change ! 2, p 0. 05 plus false discovery rate (FDR) < 5% were selected for downstream analysis. Pathway analysis was used to determine the biological pathways of the different genes using the KEGG database.
In silico analysis of OS datasets for P2RX7 expression A retrospective analysis across publicly available datasets was performed to identify P2RX7 expression in human OS cell lines. Searches were performed in the Cancer Dependency Map using the 20Q4 depmap gene expression dataset (Broad Institute, https://depmap. org/portal/), R2 Genomics Analysis and Visualization Platform using datasets (GSE86109, GSE42352, GSE11414, GSE124768 (http://r2. amc. nl) and Ordino a visual cancer analysis database https://ordino. caleydoapp. org/ where the gene P2RX7 was selected and filtered for OS, the identified cell lines were then selected for analysis.
Sections were incubated for 1 h at room temperature. After 2 washes in PBST, the sections were treated with biotinylated goat anti-rabbit IgG secondary antibody (Vector Laboratories) at 1:200 in 1% casein for 20 min at room temperature. Sections were washed twice in PBST then treated with an ABC kit (Vector Laboratories) for 20 min at room temperature and the bound antibody detected with Impact-DAB substrate-chromagen system (Vector Laboratories) for 5 min at room temperature. The sections were washed in tap water for 3 min, counter stained in Gills haematoxylin (VWR, Merck, Birmingham, UK) for 5 s, dehydrated through graded alcohols, and cleared with xylene. Coverslips were mounted using DPX. The slides were scanned using a Pannoramic 250 Flash III (3D HISTECH, Budapest, Hungary) and percentage of Ki-67 cells were quantified using QuPath software  [42].
Statistical analysis All data was analysed using GraphPad Prism v7. Datasets were tested for normality prior to analysis and statistical significance was tested using parametric or non-parametric tests as appropriate for the specific dataset. For comparing two groups, either a paired or unpaired t-test was used depending upon the groups to be compared. Two-way ANOVA was used to determine the effect of P2RX7B expression on tumour-induced changes in bone parameters in vivo. Slopes were compared using linear regression for the wound closure migration assay and a Chi-squared was used for Ki-67 staining.
1C  & 1D ). We therefore transfected both these cell lines with the truncated P2RX7B isoform (Fig. 1A  & 1B), and confirmed functional expression using P2RX7 Ca 2+ signalling and pore formation (Fig. 1C  & 1D ), the latter being unaltered as predicated. To further examine the expression of P2RX7 in OS cell lines, we performed retrospective in silico analysis using publicly available datasets. DepMap contained P2RX7 gene expression data for 14 OS cell lines, R2 genomics had data for 38 cell lines (across 4 datasets) and Ordino had data for 9 cell lines. The data was then arranged showing P2RX7 expression across the cell lines. From these datasets the expression data for cell lines relating to the HOS-TE85 family and its modified derivatives KHOS (viral), MNNG (chemical) and 143b (metastatic)  [46, 47]  were consistently low for P2RX7 expression in comparison to other OS cell lines (Supplementary Fig.
Effect of P2RX7B expression and inhibition on tumour growth and bone disease in an OS mouse model in vivo To determine whether P2RX7B expression would affect the growth and progression of OS disease in vivo a murine paratibial model of OS was used. This model has the advantage of an intact bone at the outset and results in tumours that reproduce the most common osteoblastic form of human OS  [48] [49] [50]. As TE85 cells do not form tumours in vivo, and this remained the case even after transfection with P2RX7B (data not shown), we concentrated the in vivo part of this study using the MNNG-HOS cell lines. Injection of either MNNG-HOS or MNNG-HOS + P2RX7B cells resulted in the formation of OS in the tibia (Fig. 3A ). There was no statistical difference in the final tumour size between mice injected with MNNG-HOS + P2RX7B cells compared to MNNG-HOS cells (P = 0.
8 mM ionomycin, the response was detected at excitation ratio and emission wavelength 490 nm and 525 nm respectively for five minutes. D) Measurement of plasma membrane permeabilization was performed on TE85, TE85 + P2RX7B, MNNG-HOS and MNNG-HOS + P2RX7B cells using ethidium bromide uptake, 15,000 cells in HBSS were incubated at 37 °C with or without 10 lM of the P2RX7 inhibitor A740003 for 1 h. BzATP was diluted in ultra-pure ethidium bromide to a final concentration of 300 lM BzATP and 100 lM ethidium bromide, the response was detected at 360 nm excitation and 580 nm emission for 45 min after an initial 5-minute baseline reading, with readings taken every 2 min, HEK-293 + P2RX7A was used as a positive control. All data is from 3 biological repeats with 6 technical replicates per experiment and were compared using an unpaired T-test, * = P < 0.
Fluorescence was detected at excitation 485 nm and emission 530 nm. B) TE85 compared to TE85 + P2RX7B and MNNG-HOS compared to MNNG-HOS + P2RX7B. Migration was assessed by plating 200,000 cells into a 12 well plate and left 24 h to form a monolayer, the cells were incubated in 5 lg/ml mitomycin C for 2 h and then scratched down the centre of the well using a 10 lL pipette tip, after washing twice with PBS the cells were left in medium containing 0. 5% FBS with images taken every 2 h for 24 h All images were analysed, and pseudo coloured using Tscratch software (Scale bar = 200 mm). Ci) Representative images for TE85 and TE85 + P2RX7B individually and when stimulated with BzATP, with the corresponding wound closure data shown in Ciii and CiV. Representative images for MNNG-HOS and MNNG-HOS + P2RX7B individually and when stimulated with BzATP are shown in Cii with the corresponding wound closure data shown in Cv and Cvi.
All data is from 3 biological repeats with 3-6 technical replicates per experiment and were compared using an unpaired T-test with migration slopes compared by linear regression * = P < 0. 05 ** = P < 0. 01 *** = P < 0. 001 **** = P < 0. 0001. Fig. 3. P2RX7B expression and P2RX7B inhibition on bone disease in an OS mouse model in vivo. Female BALB/c 7-9 week old mice were injected paratibially with either MNNG-HOS or MNNG-HOS + P2RX7B cells (250,000 cells suspended in 20 mL PBS). Mice were then randomised into groups and treated with either vehicle or A740003 from day 2, three times a week for 3 weeks via IP injection. Calliper measurements were taken on the final day as an end-point tumour measurement prior to euthanasia, the legs were then collected and micro-CT scanned, the total bone volume starting from the point at which the femur wasn't visible and the fibula meets the tibia was determined for each leg and normalised to its own contralateral leg.
In this study we have built upon these observations and detailed the role of the P2RX7B splice variant specifically in OS. Having previously demonstrated that the cell line TE85 does not express functional P2RX7  [15, 44]  we chose to use this cell line as well as the sub-clone MNNG-HOS to investigate the effect of the splice variant P2RX7B alone on OS cell behaviour. Prior to transfecting these cells with the P2RX7B, we confirmed that neither cell line expressed P2RX7 at the mRNA level. This finding is in direct contrast to a recent study, published during our own ongoing studies, which suggested that MNNG-HOS cells highly express P2RX7  [30]. We also scrutinised publicly available datasets to determine the relative levels of P2RX7 in the HOS family of OS cell lines and found that HOS, MNNG-HOS, KHOS and 143B cells all had low or nonexistent expression of P2RX7, further confirming our observations.
Activation of P2RX7 has been shown to induce the release of MMP13 in breast cancer cells  [55]  and has long been known to be responsible for the ATP-induced rapid release of MMP-9 from human peripheral-blood mononuclear cells  [56]. This data further supports a pro-tumorigenic role of P2RX7 in OS as demonstrated previously  [15, 30] , but adds new knowledge that the B variant alone plays a role in the metastasis cascade in OS cells in vitro. Encouraged by the in vitro data, we next examined the role of P2RX7B in OS in vivo. As previously mentioned, the TE85 cell line does not produce tumours in mice therefore the MNNG-HOS cell lines only were used. Assessment of the growth of the primary tumour using calliper measurements and Ki-67 staining did not show any effect of P2RX7B expression or any effect of the P2RX7 antagonist A740003 on the final tumour volume or proliferation status.
This was a surprising finding given the in vitro data and the previous study from Zhang et al. who showed a 50% reduction in the growth of intra-tibial MNNG-HOS tumours with A740003 treatment  [30]. The differences between our data and theirs maybe explained by the different OS models used (paratibial versus intratibial injection of cells), timing of treatment (2 days post cell injection versus $ 10 days) and also potential differences in the parental MNNG-HOS cell lines. As stated above we could not find any P2RX7 mRNA expression or typical function in the MNNG-HOS cells we used. When analysing the resultant bone disease in our OS model, expression of P2RX7B significantly affected the bone disease observed, with A740003 reducing the extent of the tumour induced bone disease in both MNNG-HOS + P2RX7B and MNNG-HOS such that the bone volume was no longer significantly increased compared to the contralateral leg.
This is in contrast to the lungs of the parental MNNG-HOS tumour bearing mice which showed no metastasis, in keeping with the previous observations that MNNG-HOS cells in vivo have no or very low incidence of pulmonary metastasis  [45, 47]. Taken together with the in vitro data of decreased adhesion with increased invasion and migration abilities of the MNNG-HOS + P2RX7B cells and the minimal effect on tumour growth seen in our in vivo studies, these data support a role for the P2RX7B in the metastasis cascade in OS. Previous studies in other cells types have elucidated various signalling pathways responsible for P2RX7 mediated effects such as via SK3 potassium channels and Cathepsin B  [17] , Cdc42 activity and the acquisition of a mesenchymal phenotype in breast cancer cells  [21] , Epithelial-mesenchymal transition (EMT) via SMAD2 phosphorylation in glioblastoma stem cells  [19]  and EMT/ invasion-related genes Snail, E-cadherin, Claudin-1, IL-8 and MMP-3 as well as PI3K/AKT and ERK1/2 in prostate cancer cells  [18].
Image analysis 2. 4. 1. Phase identification The main advantage of performing an in-situ test is that, in addition to obtaining the macroscopic responses of the material, a set of 3D images is acquired at different loading stages. Here, for each X-ray scan, a reconstructed 3D image is obtained by assembling the 2D radiographs using a filtered back projection algorithm, which is available in XAct software and provided by RX-Solutions (Annecy, France). This image represents a 3D field of X-ray attenuation coefficients inside the microconcrete specimen, which is given as a greyscale scalar function. Fig. 2  shows the mid-height horizontal slice extracted from the reference scan of the TX10-01 test (after the application of the confinement), along with the greylevel histogram of the 3D image. The shining point visible in the greyscale slice is a sign of the heterogeneity inside aggregates coming from different minerals.
These two images are "registered" (i. e. , aligned) by computing a single and homogeneous deformation function Φ which maps all of the reference image to the second one. The new difference image |f(x) -g(x)|, where g(x) corresponds to the image of the second scan after the application of the measured Φ, is shown on the bottom right of Fig. 5. The underlying meso-structure is no more visible, indicating that the two images are well aligned. After the subtraction of the measured rigid-body motion, the remaining non-zero intensity values in the difference image are an indicator of the measurement uncertainty, which is attributed to the inherent noise of the data and is intrinsic to the DVC procedure. This measurement uncertainty is quantified through a series of local DVC computations for a large range of contiguous cubic correlation window sizes.
3 ) to respectively measure the flow surface elevation and detect flow-induced seismic flume motion generated by particle impacts  (Govi et al. , 1993). The data from the geophones are recorded on a DATA-CUBE 3 logger with a sampling frequency of 800 Hz. In order to explore the properties of the seismic noise, we compute the power spectral density (PSD) of the signal recorded along the vertical by performing a fast Fourier transform with the Welch's averaging method  (Welch, 1967). According to this method the time series is split into overlapping segments (here we chose an overlap of 50 %), and the final PSD results from the average of the PSDs of each segment. We focus on sediment-transport-related seismic noise by getting rid of other sources emitted by the experimental device (e. g. water pump, water flow in pipes and on the flume) through normalizing the raw signal by the seismic power occurring under similar experimental conditions but with no sediment transport (see Sect.
e. stability) of debris deposits, we challenge the classical approach for which the sediment budget of mountain catchments is merely reduced to an available volume and hydrological conditions are considered the main factor controlling the activation of external sediment supply. Instead, the granular conditions of deposits that are coupled with mountain streams or stored in the low-slope portion of the channel should be taken into account for assessing the occurrence and dynamics of such dramatic transport events. Finally, our seismic findings challenge the application of current theoretical frameworks to inverting bedload flux from the seismic noise associated with this kind of transport process. Data availability. The data analysed during the current study are available on the Zenodo platform via https://doi.
org/10. 5281/zenodo. 5552189 (Piantini et al. , 2021h). Video supplement. The Video Supplements of this study are available on the TIB AV-Portal via https://av. tib. eu/series/1044 (last access: 3 November 2021). Video 1: Storage area with bidomal mixture, https://doi. org/10. 5446/51666 (Piantini et al. , 2021a). Video 2: Storage area with fine mixture, https://doi. org/10. 5446/51981 (Piantini et al. , 2021b). Video 3: Storage area with coarse mixture, https://doi. org/10. 5446/51982 (Piantini et al. , 2021c). Video 4: Storage area with bidomal mixture (low fraction of sand), https://doi. org/10. 5446/51984 (Piantini et al. , 2021d). Video 5: Sediment flux during the supplementary experiment, https://doi. org/10. 5446/51985 (Piantini et al. , 2021e). Video 6: Sediment pulse during the main experiment, https://doi.
Acknowledgements. We acknowledge the support of the  INRAE Research Centre of Grenoble  for the laboratory and instrumental equipment. We thank  Christian Eymond-Gris ,  Frédéric Ousset , and  Xavier Ravanat  for the technical support in the development of the flume. We thank  Maarten Bakker  for helping in the analysis of the seismic data. We thank  Guillaume Piton  for the constructive discussion on the experimental scaling of the flume. We thank the two anonymous reviewers for comments which helped improve the quality of the paper. Financial support. This research has been supported by the  Agence Nationale de la Recherche  (grant no. 17-CE01-0008 ).
[24] , an improved HR2P peptide with higher stability, solubility, and antiviral activity. The minor differences in the aminoacid sequence are identified in red, and the sequence shares 81% identify and 86% of similarity with the HR2 helix of MERS-CoV (PDB ID: 4NJL) and 46% identify and 74% of similarity with the HR2 helix of SARS-CoV-2 (as illustrated in Figure  1b ); corresponding sequence alignment is represented in Figure  S1. This peptide was also lately demonstrated to induce cross-coronaviral humoral immune response  [25, 26]. Spike protein (S protein) is mediating membrane fusion between coronaviruses such as MERS-CoV and SARS-CoV-2 and host cells  [27]. While boronic-acid modified nanostructures revealed to inhibit HCoV-229E entry and the viral replication step  [28] , Huang et al.
001 by Mann-Whitney test. Peptides were sorbed on plates and discrimination of convalescent COVID patients and pre-COVID controls was performed. The use of pancoronaviral peptide resulted in higher specificity but low sensitivity (as illustrated in Figure  8b ), while RBD peptide resulted in higher sensitivity and lower specificity of detection (as illustrated in Figure  8c ). In both cases AUROC was >80%, indicating that upon coronaviral infection there is plenty of antibodies formed targeting different parts of S-protein of the virus; thus, the use of peptides conserved among strains provides high benefits of inducing strong immune response towards currently unknown strains. Unfortunately, antibodies produced against the peptide were not able to neutralize MERSpp infection (data not shown), confirming that the HR2 region is not the major target of neutralizing antibodies.
The kinetics were measured for 3 h using BioAssay Reader HTS7000 Plus (Perkin Elmer), excitation 480/15 nm, emission 535/20 nm. Bioinformatics. The protein homology searches were done using blast (NCBI) and PDB databases. To include the regions with resolved structures in our searches, we had used SEQATOMS (http://www. bioinformatics. nl/tools/seqatoms/ using later update of 12 March 2021)  [53]. Protein structures were visualized and aligned using PyMOL (https://pymol. org/, accessed on 12 March 2021). Data analysis. ELISA testing was performed in duplicate using 2 technical replicates for each analysis (coefficient of variation [CV] always <3%). The data were normalized between plates using positive controls and corrected for background signal of secondary antibodies on each plate, then the mean values were calculated.
The mean values were used to construct data on the figures. For comparisons between two groups, the Mann-Whitney U-test for numerical variables was used. A receiver operating characteristic (ROC) curve was generated. The area under the ROC (AUROC) was calculated to estimate the specificity, sensitivity, and usefulness of the binding assays. All analyses were performed using Excel 2016 (Microsoft Corp. , Redmond, WA, USA) and Prism 8. 2 (GraphPad, San Diego, CA, USA) software. A p-value of ≤0. 05 was considered statistically significant. Four levels of significance are depicted in the figures by asterisks: * p < 0. 05; ** p < 0. 01; *** p < 0. 001; *** p < 0. 0001.
Funding: This research was funded by the  Centre National de la Recherche Scientifique (CNRS) , the  University of Lille , the  ANR , the  CPER "Photonics for Society"  and the  Agence Nationale de la Recherche  ( ANR-nanoMERS ). Financial support from the  Grant of Ministry of Healthcare of Ukraine   0119U101338  and  National Research Foundation of Ukraine   2020. 02/0131 ; Volkswagen-Stiftung  grant No  97744. This project has received funding from the  European Union 's  Horizon 2020 research and innovation program  under grant agreements No  861878.
Topsoil total Copper Datasets. Cu t datasets (Cu t, dat ; i. e. , soils within 0-30 cm) were obtained from several soil surveys across European vineyards (-9. 4° to 42° E; 35° to 53° N; SI, Figure  S1 ) delineated by the Corine Land Cover (CLC 2012; v18. 5. 1; http://land. copernicus. eu). In total, 1,202 Cu t, dat measurements (average: 27. 8 mg Cu kg -1 ; min-max: 0. 54-774 mg Cu kg -1 ) were sampled between 1992 and 2016 (median = 2008, standard deviation (SD) = 5) and used in our study. Summary of the studied Cu t, dat are provided in Table  S1  of the Supporting Information (SI). Although the Cu quantification methods differ among datasets, inter-comparability between datasets has been demonstrated previously for the methods used in our study. 22  The impact of topsoil sampling depth (first 20 or 30 cm) and sampling time span on the average prediction of Cu t (Cu pred ) at the European scale remains low (SI, section Influence of heterogeneous sampling depths and time on the Cu prediction).
Extracted data were then used to select variables and calibrate the model (details in SI). Extracted data represented adequately the range of predictive variables within the prediction domain (details given in SI; paired t-test; p-value average >0. 01) and did not display any spatial correlation (Moran's test; I average = -0. 211 ± 0. 09; p-value >0. 01). The selection of variables was carried out from the 24 original predictive variables (SI, Table  S2 ) to limit collinearity between predictive variables and optimize model predictions as described elsewhere:  37  (i) Pearson correlation was used to discard variables providing the similar information and (ii) principal component analysis (PCA) was used to discard noise variables containing the least information. 38.