dataesr/scientific-paragraphs-categorization huggingface dataset:
Importantly, the biological relevance of the transcriptional program defined by TWIST1 in the SK-N-Be2c ortho_1 xenografts was validated in human primary NB, with the identification of a TWIST1associated signature and a tumor-stroma signature, both displaying a strong prognostic impact in two cohorts of NB patients. Third, we only focused on the incidence of metastases in the lungs of mice, which occurs in approximately 4% of children with newly diagnosed NB  56. We did not detect macrometastases in the liver, one of the most frequent sites of infiltration in children together with bone marrow, bones, and lymph nodes. Fourth, the unambiguous identification of the stromal counterpart activated by the tumor-stroma signature remains challenging. Our transcriptomic data suggest an enrichment of M2 TAM and of myofibroblasts, the most abundant stromal cells supporting tumor progression, in TWIST1-positive xenografts.
gencodegenes. org/). Reads mapped on either the Human or the Mouse transcriptome were then parsed and split in one file per organism with an in-house perl script. Reads with matches on both Human and Mouse were discarded from the Mouse file. Per-gene counts and rpkm were then extracted independently for each organism using rsem version 1. 3. 0. All RNAseq per-gene data quality checks and analysis were done in R. Mouse and Human data were analyzed independently, but following the same protocol. Protein coding genes with a log2 (rpkm) value above 1 in at least one sample were kept (13742 genes in SK-N-Be2c for Human data; 14538 for Mouse data). PCA were done using the normalized log2 (rpkm) values. Clustering analysis were performed on the normalized log2 (rpkm) values using euclidean distance measures and the ward.
D2 agglomeration method. Differential analyses were performed using the raw counts in DESeq2 package version 1. 26. 0. For each comparison, the cutoffs for fold-change (in log2) and adjusted p values to call differentially transcribed genes were set to 1 and 0. 05 for Human, respectively, and to 0. 5 and 0. 05 for Mouse, respectively. Heat maps for sample correlations and for specific gene lists were generated using the heatmap. 2 function from the gplots package version 3. 0. 1. 2 on the log2 of DESeq2 normalized counts. Functional gene ontology analysis was performed by applying a hypergeometric test on selected genes lists against gene sets from KEGG, GO (Molecular Function, Biological Process, and Cellular Component), REACTOME, and BIOCARTA pathways. The p value cutoff for terms selection was set to 0.
001 for Human data and 0. 01 for Mouse data; only those terms with an adj p value below 0. 01 and 0. 1 were taken into consideration for the graphical representation, respectively. For the GO analysis of the secretome, the lines containing multiple gene references were split before to apply the hypergeometric test on the resulting list of genes (673 terms in the secretome vs 678 terms in the transcriptome). For external RNAseq data analysis (Super series number: GSE80154; SubSeries number: GSE80153), fastq files from GSM2572350 to GSM2572355 corresponding to Be2C samples at 0 (DMSO: GSM2572350 to GSM2572352) and JQ1 24 h (GSM2572353 to GSM2572355) were downloaded. These samples were then re-analyzed by applying the same protocol used for the local RNAseq data. xCell analysis was performed on the Mouse RNAseq normalized counts using the online xCell server (https://xcell.
Mass spectrometry data analysis and processing. Tandem MS data were processed by the MaxQuant software (version 1. 6. 3. 4))  66 incorporating the Andromeda search engine  67. The UniProt human reference proteome database of January 2019 was used (73,950 sequences), supplemented with sequences of common contaminants. Trypsin (cleavage at K,R) was used as the enzyme definition, allowing two missed cleavages. Carbamidomethylation of cysteine was specified as a fixed modification. N-terminal acetylation of protein and oxidation of methionine were specified as variable modifications. All identifications were filtered at 2% FDR at both the peptide and protein levels with default MaxQuant parameters. After inspection and data QC based on the Ibaq 68 values, the LFQ label-free values  69  were used for protein quantitation.
MaxQuant data were further processed with Perseus software  70  for the filtering, log2-transformation, normalization of values, and the statistical analyses. After removal of contaminants and reverse hits, intensity values were log2 transformed. Only proteins identified by at least two peptides and quantitated in at least all three samples of one condition were retained for further analysis. Missing values were imputed with standard Perseus parameters (normal distribution with width 0. 3 and down-shifted by 1. 8 SD). An unpaired T-test was used to determine significant changes, corrected for FDR with the Benjamini-Hochberg method and a threshold q-value at 0. 01. Imputed values were subsequently removed from tables. Gene Ontology functional analysis were performed as previously described in the "Bioinformatics analysis" section, after splitting the lines containing multiple genes references.
Acknowledgements We thank  Dr. Manfredo Quadroni  ( Protein Analysis Facility, University of Lausanne ) and his team for their help with the secretome analysis. Dr. Jessica Dessimoz  (Histology Core Facility of the EPFL) and  Janine Horlbeck  ( Mouse Pathology Facility ) for their help with the IHC and tissue staining. Dr. Julien Marquis  ( Lausanne Genomics Technologies Facility ) for his technical advice in the targeted sequencing analysis of the indels in TWIST1 gene. This work was supported by grants from the  Stiftung Kinderkrebsforschung Schweiz  (to A. M. M. ), the  Novartis Foundation for Medical-Biological Research  (to A. M. M. ), the  Hubert Gouin Association  (to A. M. M. ), and the  FORCE foundation  (to A. M. M. and R. R. ).
Data availability All data generated during this study are included in this article (and its Supplementary Information file). The RNAseq data can be accessed at the GEO public repository using the accession number GSE160765, the mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD024200 (www. proteomexchange. org); and the images datasets at the Zenodo repository with the https://doi. org/10. 5281/zenodo. 5658524  71 and https:// doi. org/10. 5281/zenodo. 5658345  72 , respectively. The RNAseq data of SK-N-Be2c JQ1 samples were obtained from GEO, using the accession number GSE80153. NGS sequencing data for the indels obtained upon TWIST1 gene editing by CRISPR/Cas9 are provided in Supplementary Data 8.
Data Samples and Simulations The analysis is based on hybrid data collected by the Coihueco and HEAT telescopes and the 750 m SD array between 2010 June 1 and 2015 December 31. Subsequent data will be used in a follow-up paper. In the present paper, we use the same analysis techniques as in  Aab et al. (2017a)  to provide a first search for photons in the energy range between 2 × 10 17 and 10 18 eV using data from the Pierre Auger Observatory. The follow-up paper will not only make use of a larger data set, but will also profit from an analysis that is tailor-made for the lowenergy enhancements of the Observatory. Several selection criteria are applied to this data set to ensure a good reconstruction of the air-shower events and a reliable measurement of the observables used to discriminate photonand hadron-induced air showers (see Section 4).
g. ,  Yushkov & Pierre Auger Collaboration 2019) , the assumption of a pure-proton background in the context of a search for UHE photons can be taken as a conservative worstcase assumption, since including heavier nuclei would always lead to a smaller estimate for the contamination in the final sample of photon candidate events. All simulated air-shower events are processed with the Auger Offline Software Framework  (Argiro et al. 2007 ) for a detailed simulation of the detector response. In these simulations, the actual detector status of both the SD and the FD as well as the atmospheric conditions at any given time during the aforementioned data period are taken into account, leading to a realistic estimate of the detector response. Each simulated air shower is used five times, each time with a different impact point on the ground, randomly taken from a uniform distribution encompassing the region of the 750 m SD array, and with a different event time, which was randomly determined according to the on-time of the Coihueco and HEAT telescopes during the data period used in this analysis.
2019/10151-2 ,  2010/07359-6 , and  1999/05404-3 ;  Ministério da Ciência, Tecnologia, Inovações e Comunicações (MCTIC) ;  Czech Republic -grant Nos. MSMT CR LTT18004 ,  LM2015038 ,  LM2018102 ,  CZ. 02. 1. 01/0. 0/0. 0/16_013/0001402 , CZ. 02. 1. 01/0. 0/0. 0/18_046/0016010 , and  CZ. 02. 1. 01/0. 0/0. 0/17_049/0008422 ; France-Centre de Calcul IN2P3/CNRS ;  Centre National de la Recherche Scientifique (CNRS) ;  Conseil Régional Ile-de-France ;  Département Physique Nucléaire et Corpusculaire  ( PNC-IN2P3/CNRS );  Département Sciences de l'Univers (SDU-INSU/CNRS) ;  Institut Lagrange de Paris (ILP)  grant No. LABEX ANR-10-LABX-63  within the  Investissements d'Avenir Programme  grant No. ANR-11-IDEX-0004-02 ;  Germany-Bundesministerium für Bildung und Forschung (BMBF) ;  Deutsche Forschungsgemeinschaft (DFG) ;  Finanzministerium Baden-Württemberg ;  Helmholtz Alliance for Astroparticle Physics (HAP) ;  Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF) ;  Ministerium für Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen ;  Ministerium für Wissenschaft, Forschung und Kunst des Landes Baden-Württemberg; Italy-Istituto Nazionale di Fisica Nucleare (INFN) ;  Istituto Nazionale di Astrofisica (INAF) ;  Ministero dell'Istruzione, dell'Universitá e della Ricerca (MIUR) ;  CETEMPS Center of Excellence; Ministero degli Affari Esteri (MAE) ;  México-Consejo Nacional de Ciencia y Tecnología (CONACYT)  No.
The numerical results are supported with theoretical analysis of the newly implemented distribution function, following the dispersion relation studies carried out in  [6, 8, 19]  (Section 4). Finally, experimental relevant distributions functions from Fokker-Planck solver code RABBIT  [28]  are presented and later used to obtain realistic simulations of NLED-AUG case  [29]  with experimental density and temperature profiles. Results are qualitatively compared with NLED-AUG case experimental data  [30]  and then discussed (in Section 5).
Shot 31213 has the most off-axis angle (7. 13 • ), shot 31214 the most on-axis (6. 07 • ) and 31215-6 a mid-range angle (6. 65 • ). In order to achieve experimental relevant scenarios, these distribution functions were given as input to the gyrokinetic code ORB5 with the realistic profiles of density and temperature from the experimental setup of the different shots. The EP realistic profiles from the four shots are represented in Figure The results obtained from ORB5 using the RABBIT distribution functions are shown in Fig. 17. As we notice, the growth rates are all negative. In fact, such NBI angles correspond to high ξ 0 values and, as we have seen from Section 3, such high values of ξ 0 produce rather stable modes. 16.
7 Acknowledgment This work has been carried out within the framework of the  EUROfusion Consortium  and has received funding from the  Euratom  research and training program 2014-2018 and  2019-2020  under grant agreement No  633053. The views and opinions expressed herein do not necessarily reflect those of the European Commision. Part of this work is supported by  R&D Program  through the  Korean Institute of Fusion Energy (KFE)  funded by the  Ministry of Science and ICT of the Republic of Korea  ( KFE-EN2141-7 ). Simulations presented in this work were performed on the MARCONI FUSION HPC system at CINECA and the  HPC systems of the Max Planck Computing and Data Facility (MPCDF).
Paramedics often rely on the interpretation skills of bystanders or try to communicate in a third language, for example, English  [7, 8]. Ad hoc translators, such as Google Translate, are still not considered sufficiently accurate for translational services in health settings  [9, 10] , especially in lesser used languages  [11]. Moreover, such services often require reliable network coverage, which is rarely guaranteed in rural areas in Germany. Misunderstandings in the medical history and misinterpretation of symptoms can lead to severe errors and jeopardizes the safety and quality of provided emergency treatment  [12] [13] [14]. Research has shown that lack of language interpretation leads to ineffective use of resources  [15]  and can cause delays in the delivery of care  [16] [17] [18].
Alternatively, the information received can be presented in a structured way using the SAMPLE history scheme (assessment used in prehospital emergency care including Symptoms, Allergies, Medications, Past medical history, Last oral intake, Events prior to incident). For this study, the app is run on a Motorola Play Z2 Android smartphone with external speakers to be of use in noisy environments. All phrases were translated and audio-recorded by professional interpreters. In this study, the app supported the following 18 languages: Arabic, Bosnian, Croatian, Czech, Dari (Persian), English, Farsi (Persian), French, German, Italian, Kurdish-Sorani, Lithuanian, Pashto (Afghani), Polish, Russian, Serbian, Spanish, and Turkish.
While this difference was not significant, it suggests a tendency that the use of the app may increase on-scene time. In a previous study, it was shown that paramedics who have used the app in patient care perceive it as less complex and feel more confident about using the app  [22]. Other studies suggest that on-scene time is reduced with patients with limited proficiency in the locally spoken language  [25] , potentially due to less time spent communicating to patients. Fixed-phrase translation apps for EMS showed to have good usability  [22]  and were preferred over direct translation devices such as Google Translate (Alphabet Inc) by foreign language speakers  [26]. To the authors' knowledge, this is the first study that assessed the impact of such an app on the quality of communication in a real-life setting.
Acknowledgments We sincerely thank the paramedics of the rescue stations in Königslutter, Wendhausen, Helmstedt, and  Braunschweig  for their participation. We are grateful to the team at aidminutes GmbH, in particular to the app's main software designer,  Philipp Geisler , for their commitment. We acknowledge the support of the  Malteser Hilfsdienst gGmbH , the district of Helmstedt, and the  Fire Department of the City of Braunschweig. We also thank  Thomas Wächter  from the  District of Helmstedt and Heinz Hagengers  ( CKS Systeme GmbH ), who provided support and advice on data export. We also want to credit the efforts of  Jennifer Schulze  and  Luise Wehl , who were mainly involved in performing the chart reviews of the paper-based Rescue Service Case Protocols. The study was funded by the  Federal Office for Agriculture and Food (BLE)  of the  German Federal Ministry of Food and Agriculture  (grant  2818LD007 ) on the basis of a resolution of the  German Parliament , the  Ministry for Social Affairs, Health and Equity of Lower Saxony  (grant  5SL1.
All these objects were subjected to mineralogical characterization, mainly by Raman spectroscopy, but also by other methods when necessary. These analytical approaches have been particularly important in clarifying the mineralogical natures of the rocks used by the Amerindians. This is illustrated, for example, by the demonstration of the use of sudoite, a mineral of the chlorite family, for the production of several objects found in several archaeological sites. This material, unknown in the world as a gemstone, was thus the subject of a particular study in order to confirm this gemological attribution  (Queffelec et al. , 2021a). All these first-hand data and data from an intensive bibliographic search were integrated into a database. The structure of this database is based on 4 tables (islands, sites, beads, sources) and has been published in a dedicated article  (Queffelec et al.
, 2021b)  following recommendation by Peer Community In Archaeology  (Marwick, 2021). The coding system in the database (also used in Figures  1 to 5 ) is constructed as follows. It starts with two letters corresponding to the island on which it was found, followed by a two-digit number corresponding to the number of the site on that island, and finally a three-or four-digit number representing the number of the object in that site. Thus, object GD-02-003 corresponds to the third object (003) studied from Morel (02), an archaeological site located in Guadeloupe (GD). In order to disseminate this information to all interested researchers, online tools were used. This database is available online in English and French as a spreadsheet (https://osf. io/qbnkm and https://osf. io/zpwt8 respectively), and in the form of a Filemaker online database (Figure  6 ) accessible at this address: https://fm02.
Only five sites account for of the objects classified as raw material, but it should be noted that the absence of a count of raw material shards in the very rich sites of Puerto Rico and Vieques, although indicated as being present "in large quantities" (Narganes Storde, 1995), obliterates a certainly not insignificant part of the archaeological record because they cannot be included in our database. The more rarely identified object types include unperforated plates, bead-pendants, which are mostly longitudinally and transversely perforated cylinders, a few unidentified objects (often because they are still preforms), and, finally, labrets, which are rather thin and long objects, but whose attribution as a labret remains speculative. Among the different types of beads, the most numerous are the discoid kind, followed by cylindrical ones (Figure  13 ).
Plano-convex beads were found in similar numbers to barrelshaped beads, the other types being much rarer. In view of the collections studied in detail on the French Caribbean islands, this third position of plano-convex beads is surprising. However, it should be noted that their number is mainly driven by a few sites such as Sorcé -La Hueca which accounts for 72% of their numbers, while barrel-shaped beads are more evenly distributed although the Pearls site accounts for 56% of the total. The lapidary production of pendants in the Ceramic period is largely dominated by zoomorphic forms (91% of the corpus) among which frogs are widely prevalent (Figure  14 ). Geometric pendants of various shapes are the second most common type. Other forms are very rare and not very diverse. It must also be noted that, although this database certainly lists a very large of the archaeological sites of the Ceramic period that have yielded stone ornaments, there is still considerable room for improvement in the data it contains.
Another current limitation to be highlighted I that the distribution of the raw materials used clearly indicates the predominance of the indeterminate in the database: they represent almost half of the corpus! This lack of knowledge further underlines the need for additional studies including precise raw material identification to increase the strength of our interpretations of diffusion networks in the future, especially in the richer sites that have not been subject to such work. When focusing on the different raw materials identified so far, the corpus is largely dominated by diorite and serpentine, followed quite far behind by rock crystal and then by a group formed by calcite, carnelian, jadeite, turquoise and amethyst (Figure  15 ). As this database is largely based on an inventory drawn from the literature, these proportions of material differ from those that can be established solely from the set of sites located in the French islands where the raw materials have been systematically analyzed  (Queffelec et al.
Discussion et conclusion By combining the analytical characterization and comprehensive documentation of Ceramic period lapidary production in the French islands of the Antilles with an intensive review of the scientific literature on the subject for the other islands, the establishment of a database of lapidary production at the scale of the islands of the Antilles allows for the robust validation of ideas that have already been established for a long time by archaeologists of the Caribbean area. It is now possible to attest and quantify that the Early Ceramic and Early/Middle Ceramic periods provided far more lapidary artifacts than the more recent periods, as already observed by several authors  (Bérard, 2013; Hofman et al. , 2014 Hofman et al. , , 2007;; Knippenberg, 2007; Rodríguez Ramos et al.
, 2013). Beyond this first chronological approach, such an inventory also makes it possible to highlight other information in terms of typology and raw materials used: beads are twice as numerous as pendants, discoid beads largely dominate over cylindrical beads, pendants are more than 90% zoomorphic and 85% of them represent frogs. Finally, this work has also highlighted the very important work that remains to be done on these objects, both in terms of mineralogical characterization (almost half of the beads are not determined at this level) and detailed typological documentation. Further studies of these data are planned in order to compare more precisely the distribution of types, raw materials, and combinations of these two parameters, in time and space. For this, diversity analyses, ordering by means of seriations, comparisons thanks to correspondence analysis comparisons, and network analyses will be performed.
Such documentation could also allow stylistic studies on pendants, by making a large number of photographs accessible to the greatest number of people, although on this point too, much work remains to be done. Our proposal to use open online tools will hopefully encourage Caribbean archaeologists to participate in making the database even more exhaustive. It is indeed always possible to add new data and this database will be updated regularly, in particular during future studies of archaeological series from sites located outside the French islands of the archipelago.
Acknowledgments The authors of this article wish to thank all the archaeologists who conducted the fieldwork and therefore permitted this type of study to exist. We also thank all the people who made it possible for us to access the archaeological artifacts in museums and curation centers:  Susana Guimaraes ,  Katarina Jacobson , and  Jean-Luc Bernos  ( Musée Edgar Clerc ),  Thierry Dorival  ( DAC Martinique ),  Gwenola Robert  ( DAC Guadeloupe ),  François Petit  (owner of  Hope Estate ),  Peggy Deroze  and  Claudia Daribo  ( Musée d'Archéologie et de Préhistoire de Martinique ). The study of the archaeological artifacts would not have been possible without the help of Christian Stouvenot et  Gwenola Robert  ( DAC Guadeloupe ),  Susana Guimaraes ,  Katarina Jacobson  ( Musée Edgar Clerc ),  Thierry Dorival  ( DAC Martinique ), et  François Petit  (owner of Hope Estate).
We also would like to thank  Philippe Jullien  and  Jean-Philippe Droux  for their help with the integration of the database in ArkeoGIS. This work was carried out within the framework of the  Programme Collectif de Recherche Parures Amérindiennes dans les Antilles Françaises , funded by the  Ministry of Culture (DAC Guadeloupe and DAC Martinique)  and the  Region of Guadeloupe. This work benefited from the environment of the GPR Human Past.