dataesr/scientific-paragraphs-categorization huggingface dataset:
PK receives financial support by the  Hungarian Brain Research Program   2017-1. 2. 1-NKP-2017_VI/4. MRA received funding from  NIMAD , proposal No 971846. JB is supported by a  Senior Clinical Researcher mandate of the Research Fund-Flanders (FWO)  under grant agreement number  1805021N  and is a member of the µNEURO  Research Centre of Excellence of the University of Antwerp. Several authors of this publication are members of the European Reference Network for  Rare Neuromuscular Diseases (ERN EURO-NMD ) and of the  European Reference Network for Rare Neurological Diseases (ERN-RND). RR and the  University of Auckland CBR Neurogenetic Research Clinic  receive funding from the  Friedreich's Ataxia Clinical Outcome Measures study and the Duncan Foundation (NZ).
PROSPAX hereby utilizes a "spin-off " Pseudonym Patient's pseudonym study registry version, which directly builds on the ARCA Personal information Date of birth ( )* Registry, with fully compatible pseudonymization procedure and Sex at birth eCRFs, and where datasets will be integrated into the ARCA Patient status Alive or dead Registry (and equally the HSP registry) at the end of the Date of death study. PROSPAX also draws on all the other components of Care pathway First contact with specialized center the multi-component ARCA database cluster described above Disease history Age at onset of first symptoms/signs (ARCA biomaterial database, GENESIS, and ARCA multi-study Age at diagnosis or first consultation database). Diagnosis Diagnosis of rare disease in Orpha code Genetic diagnosis in HGVS Undiagnosed case in HPO terms Research Agreement to be contacted for research Consent to reuse data for other research Biological sample available Link to biobank where biosample is stored Disability Classification of functioning/disability *Restricted to year of birth.
Using the extended site network and longitudinal dataset provided by the ARCA Registry, PREPARE has run phenotype and natural history studies on several ARCAs, e. g. , RFC1 (24), COQ8A/ADCK3 (25), RFC1, POLG (26), and PRDX3 (27). PROSPAX The network PROSPAX (An integrated multimodal PROgression chart in SPastic atAXias), launched in 2020 and funded by the European Joint Program on Rare Diseases (EJP RD), will establish a paradigmatic integrated trial-ready model of disease progression and mechanistic evolution in spastic ataxias. It hereby builds on a rigorous trial-like multicenter natural history.
Observation sets Most data sets used in this work were already processed in  Lainey et al. (2007)  and  Jacobson (2010) , and benefited greatly from the astrometric catalogue of  Morley (1989). A large astrometric database is available on the Natural Satellites DataBase (NSDB) server  (Arlot & Emelyanov 2009). It turned out that some of the old measurements were extremely biased and therefore were eventually not included in the fit. Moreover, ground observations with residuals larger than 2 arcseconds were removed. A rejection criteria beyond 3σ was applied to ground observations. Last, spacecraft data were weighted in the same way as in  Lainey et al. (2019). Here we present two important new data sets, not available to the former works.
The image positions of stars have been determined by fitting a 2D Gaussian profile to the pixel value distributions  (Duxbury 2012, pers. comm. ). Pointing corrections have been derived w. r. t. the predictions of reference star positions based on the UCAC4 catalog. The directions to Phobos have been measured by applying the limb-fit approach based on the latest 3D shape model by  Willner et al. (2014). Between May 2013 and March 2014 a larger number of flybys than usual have been performed in order to support the Phobos gravity field experiment. Therefore data from 38 approach maneuvers with distances ranging from 350 to 14 000 km have been evaluated. Summing all up, 340 astrometric observations of Phobos in right ascension and declination coordinates have been provided. Estimated uncertainties vary from hundreds of meters up to one km  (Pasewaldt et al.
(2014)  and  Thomas et al. (2000) , respectively. To achieve a better agreement with the observation, the simulation is convolved with a point spread function describing the image distortion of the SRC. Here a subset of the PSF derived by  Duxbury et al. (2011)  was applied. Matching the illuminated simulation against the observation provides the bodies' line and sample coordinates with sub-pixel accuracy. For images showing either Phobos and/or Deimos with a far distant object, the derived right ascension and declination of the moon (as seen from MEX) are determined. The exhaustive list of MEX data we used is given in Table  4. In particular, due a current limitation of our software, mutual events evolving both moons simultaneously (i. e. without the presence of Jupiter or Saturn) have not been included in the current solution.
Conclusions We developed new ephemerides of Phobos and Deimos, fitted to the largest time span of observations, including recent unpublished astrometric data obtained by evaluating images taken by the HRSC aboard Mars Express. During the fitting process, we could solve for the physical libration of Phobos, found to be equal to 1. 09 ± 0. 01 degrees. Considering the very low uncertainty, this may suggest to consider higher order harmonics with an improved rotation model in the future. We confirmed an inconsistency between recent Mars Reconnaissance Orbiter and Mars Express data on Deimos observations. Since Mars Reconnaissance Orbiter's observations were performed from a large distance we imputed the inconsistency to an erroneous center of figure determination. Our ephemerides NOE-4-2020 are available in SPICE format directly from ftp://ftp.
imcce. fr/pub/ephem/satel/NOE/MARS/2020/. Acknowledgements. The authors are indebted to O. Witasse, R. Jacobson and S. Le Maistre for fruitful discussions. This work has been supported by the European Community's Seventh Framework Program (FP7/2007-2013) under grant agreement 263466 for the FP7-ESPaCE project. The authors wish to thank the HRSC Experiment team at DLR, Institute of Planetary Research, Berlin, and at Freie Universität Berlin, the HRSC Science Team, as well as the Mars Express Project teams at ESTEC, ESOC, and ESAC for their successful planning, acquisition, and release of image data to the community. A&A proofs: manuscript no. Lainey-Mars-moons_rev1 1870 1880 1890 1900 1910 1920 1930 1940 1950  Time (years)     0. 843538311722695 ± 1. 09E-5 -0. 178915197575563 ± 1. 10E-5 Table  7.
This recognition, which is performed by a convolutional neural network (Affouard 2017), allows the user to get a list of candidate species, each associated with a confidence score. The second component of Pl@ntNet's workflow is the enrichment of the database to improve the observation quality of the data collected. Because of the huge volume of data (over four million observations shared in 2020, Pl@nt Net statistics), this enrichment cannot be done solely by expert botanists.
various crowdsourcing mechanisms have been put in place allowing the collaborative curation the data. The third part of the Pl@ntNet workflow is the exploitation of the database, which is made available for the needs of stakeholders such as researchers. For example, the recent sharing of Pl@ntNet data on GBIF's (Global Biodiversity Information Facility) platform, through two complementary datasets, has increased the benefit to the scientific community (examples are available here). To support the development of customized e-floras, three complementary concepts have been developed: micro-projects, groups, and monitoring work spaces, whose services are detailed below: (a) Micro-projects allow full adaptation of the interfaces of the Pl@ntNet apps to a species list of interest. This e-flora can be linked to a specific geographical area, which allows it to be automatically selected according to the user's location.
Over 260 groups have already been created by e. g. , professional land managers, educators, and plant enthusiasts. (c) Monitoring work spaces allows a given stakeholder to access all the observations and identification requests of a given species list in a particular area. Micro-projects and Groups only allow exploration of plant observations explicitly shared by the authenticated users. However, Pl@ntNet's database contains hundreds of millions of plant identification requests submitted by anonymous users. Monitoring work spaces was set up to allow access by land managers to this rich and important material. These work spaces provide the maps, the list of plant observations, and identification requests (with a very high confidence score on the species identification), for all the species of interest to a given partner.
Juvenile myelomonocytic leukemia (JMML), a rare myelodysplastic/myeloproliferative neoplasm of early childhood, is characterized by clonal growth of RAS signaling addicted stem cells. JMML subtypes are defined by specific RAS pathway mutations and display distinct gene, microRNA (miRNA) and long non-coding RNA expression profiles. Here we zoom in on circular RNAs (circRNAs), molecules that, when abnormally expressed, may participate in malignant deviation of cellular processes. CirComPara software was used to annotate and quantify circRNAs in RNA-seq data of a "discovery cohort" comprising 19 JMML patients and 3 healthy donors (HD). In an independent set of 12 JMML patients and 6 HD, expression of 27 circRNAs was analyzed by qRT-PCR. CircRNA-miRNA-gene networks were reconstructed using circRNA function prediction and gene expression data.
Patients Total RNA from diagnostic bone marrow (BM) or peripheral blood (PB) samples from 31 children with JMML was obtained from different institutions throughout Europe (Belgium, Netherlands, France, Czech, and Germany). None of the patients received prior treatment (Supplementary Table  1 ). Additionally, BM and PB from pediatric healthy donors (HD); (siblings screened for transplantation) were collected from 9 healthy subjects at the Ghent University Hospital (Supplementary Table  1 ). The "discovery cohort" used for RNA-seq profiling comprised 19 JMML and 3 HD. Results were validated in an additional cohort of 12 JMML patients and 6 HD. Out of 31 JMML patients, 15 are registered in the European Working Group of Myelodysplastic Syndromes in Childhood (EWOG-MDS) studies EWOG-MDS98 and EWOG-MDS2006 (National Institutes of Health trials registered as #NCT00047268 and #NCT00662090 at www.
CircRNA Differential Expression Circular RNAs expression was normalized with the regularized logarithm method  (Love et al. , 2014) , and the surrogate variables were estimated with the sva R package  (Leek, 2014)  in order to remove hidden batch effects. Differential expression in pairwise comparisons between conditions or sample groups was assessed by DESeq2  (Love et al. , 2014) (v1. 22. 2 ) with local fit model including Wald significance tests, no independent filtering and correction for surrogate variables. P-values were corrected for multiple tests with the Benjamini Hochberg procedure, and an adjusted p-value ≤ 0. 05 was chosen to detect significant differential expression.
CircRNA-miRNA-Gene Network Reconstruction Putative circRNA sequences were assembled joining annotated exons contained in the genomic coordinates corresponding to the validated backsplice ends. MiRNA binding sites were predicted through miRanda  (John et al. , 2004 ) (score ≥ 100 and free energy ≤ -20 kcal/mol) and PITA  (Kertesz et al. , 2007)  ( G duplex < -20 kcal/mol and G open > -13 kcal/mol), keeping only miRNAs with commonly predicted binding sites. MiRNAs were subsequently prioritized according to expression in a published series of 21 JMML patients [GEO Series accession number GSE71452  (Helsmoortel et al. , 2016) ]. For recently identified miRNAs, not quantified in the series, at least three predicted binding sites for the same circRNA were required. Validated miRNA target genes (strong miRTarBase validation categories) were retrieved by Mienturnet web tool  (Licursi et al.
Quantification of circRNAs by qRT-PCR Synthesis of cDNA was performed after an additional insolution gDNase elimination step (Heat&Run gDNA removal kit, ArcticZymes), using the 5x PrimeScriptTM RT Master Mix (Takara Bio Europe S. A. S. ). All qRT-PCR reactions were carried out with custom designed primers (Supplementary Table  2 ) in 96-well plates using the Takyon qRT-PCR MasterMixes for SYBR assays (Eurogentec) on a Viia7 analyzer (ThermoFisher). TBP, HPRT1 and GAPDH were used as internal reference genes. Ct thresholds were automatically determined by the QuantStudio TM Real-Time PCR Software and data analysis was performed according to state-of-the-art methods. Briefly, Ct values generated for each target were corrected for primer pair efficiency and expressed as relative quantities (RQ).
CircRNAs Expression in Patients With JMML and Healthy Donors A cohort of 19 JMML patients representing the four main subtypes (8 PTPN11, 5 KRAS, 4 NRAS, and 2 NF1 samples; Supplementary Table  1 ) was analyzed together with 3 agematched healthy donors (HD; GEO ID: GSE147523) to study circRNA expression in patients with JMML. Quantification and annotation of circRNAs, from high-depth ribo-depleted RNA-seq data, by CirComPara  (Gaffo et al. , 2017)  detected 43,757 circRNAs, of which 5,323 with high expression were considered for further investigation (see section "Materials and Methods"). These circRNAs derived from 2,585 loci, mostly from exonic regions (95. 5%), followed by gene introns and genomic regions without known genes (Figure  1A ). Overall, 1,133 (43. 8%) circRNA host genes expressed multiple circular isoforms each, with 28 genes expressing 10 up to 23 isoforms (Supplementary Figure  1  in Supplementary Material).
ETHICS STATEMENT The studies involving human participants were reviewed and approved by Out of 31 JMML patients, 15 are registered in the European Working Group of Myelodysplastic Syndromes in Childhood (EWOG-MDS) studies EWOG-MDS98 and EWOG-MDS2006 (National Institutes of Health trials registered as #NCT00047268 and #NCT00662090 at www. clinicaltrials. gov), and 16 in the French national JMML biobank. Written informed consent was obtained from the parents or legal guardians of patients before sample collection and in accordance with the Declaration of Helsinki. The study approval was granted from the institutional review committee at the Ghent university hospital (EC/2011/825) and at each participating center. Written informed consent to participate in this study was provided by the participants' legal guardian/next of kin.
, 2002). This is supported by the correlation between the PAH content and soil characteristics for soils in urban parks, as urban areas have highly concentrated PAH emissions from sources such as road traffic, industries, and residential emissions  (Cachada et al. , 2012b; Keyte et al. , 2016). However, considering that five soils in this study were collected from urban parks, a similar conclusion cannot be made based on our data set. At the scale of the entire country, the influence of soil characteristics on PAH content would be minimised by the proximity of major emission sources  (Aichner et al. , 2013). In addition to soil physicochemical characteristics, relationships between the PAH content in soils and land use type have been noted in some studies (Maliszewska-Kordybach, 1999); however, no differences in PAH content were observed among forests, cultivated lands, and permanent pastures in this study (see Fig.
, 2015). In France, a database of 300 urban soils was created (ADEME, 2018), and the soils therein had a median value of 1560 µg kg -1 in the 16 PAHs, which is 50 times higher than the 32 µg kg -1 in the 15 PAHs in the current study. Therefore, the higher risks posed by PAHs in soils would be expected in urbanised regions. In addition, the distribution of soils with higher TLCRs around cities (especially Paris, Lille, and Marseille) highlights the influence of densely urbanised areas on the surrounding soils over a distance of up to several dozen kilometres  (Jensen et al. , 2007). Finally, the 20 sites with the highest TLCRs above 10 -6 appeared to be randomly distributed throughout the territory, suggesting local sources of PAHs at those sites, such as heavy industries. The first results of the background national health risks linked to PAHs show the spatial heterogeneity in the risks encountered by the population and the necessity of considering soils in risk evaluations and the national surveillance of contaminants in the environment.
Acknowledgements. The soil sampling and the analyses of physicochemical properties of soils were supported by the  French Scientific Group of Interest  on soils, GIS Sol, involving the  French Ministry in charge of the Ecological Transition (MTE) , the  French Ministry in charge of the Agriculture and Food (MAA) , the  French Agency for Environment and Energy Management (ADEME) , the  French Biodiversity Agency (OFB) , the  National Institute of Geographic and Forest Information (IGN) , the  French National Research Institute for Sustainable Development , and the  National Institute for Agronomic and Environmental Research (INRAE). We thank all the soil surveyors and technical assistants involved in sampling the sites. Financial support. The PAH analyses were supported by a grant from the  French Observatory for the Pesticide Residues (ORP).
Code availability. The R code used to spatialise the data has been published in a repository of the research institute IN-RAE. This code can be accessed through the following DOI: https://doi. org/10. 15454/BJFUEV (Saby et al. , 2021). Data availability. The data used in the paper are available at: https://doi. org/10. 15454/WPR2C9 (Froger et al. , 2021). A raster file in Geotiff format containing the geo-refenced data of PAH sums after spatialisation is also available with the data set. Supplement. The supplement related to this article is available online at: https://doi. org/10. 5194/soil-7-161-2021-supplement.
a Sea surface temperature (SST, °C) showing the study site (yellow star) and other core locations mentioned in the text (white circles), together with the Southern Ocean and the southern Indian Ocean fronts: Subtropical Front (STF), Subantarctic Front (SAF) and Polar Front (PF)  2, 74  , and the schematic representation of the average surface ocean circulation (Agulhas Current, AC; Agulhas Return Current, ARC; Agulhas Leakage, AL)  75. b Chlorophyll-α concentrations (mg m -3 ). c Coccolithophores (mg m -3 ). d Diatoms (mg m -3 ). Data, maps and visualisations were generated using the Giovanni online data system (https://giovanni. gsfc. nasa. gov/giovanni/) developed and maintained by the National Aeronautics and Space Administration Goddard Earth Sciences Data and Information Services Center (NASA GES DISC)  30.
The SST and chlorophyll data are derived from Moderate Resolution Imaging Spectroradiometer on the Aqua satellite (MODIS-Aqua) provided to Giovanni by the Ocean Biology Distributed Active Archive Center (OB. DAAC). The coccolithophore and diatom data are from the NASA Ocean Biogeochemical Model (NOBM)  76. Southern Ocean, where CO 2 exchange between the ocean and atmosphere is especially high, deep waters enriched in respired CO 2 and nutrients are brought to the surface by vertical mixing (e. g. wind-driven upwelling)  5, 6  , promoting high rates of phytoplankton productivity in the photic layer  7. However, it is thought that the efficiency of CO 2 outgassing from the ocean to the atmosphere through the biological pump is controlled by ambient physico-chemical properties of the water column  8  and the abundances of different phytoplankton groups in the upper ocean  5, 9.
In particular, the UPZ coccolithophore community shows distinct peaks during insolation maxima (Fig. 5b ), indicating that the upper water column conditions over the Agulhas Plateau is influenced by insolation intensity in high latitudes, specifically the SH, driving seasonal variability in the upper ocean biotic communities. Reconstructed productivity records from both geochemistry (C 37:3-2 alkenone abundances and MARs) and independent coccolith data also reveal dominant periodicities (significant at 95% confidence interval, CI) related to the 100-kyr eccentricity (Supplementary Figs. 2  and 3 ). Weaker spectral peaks at 41-and 23-kyr periodicities are recorded for alkenones and primary productivity, corresponding to obliquity and precession, respectively. A total absence of obliquity signal is found in the record of total coccolith abundance as well as on the assemblage-derived productivity (Npp), and water column stratification proxies (F.
Significance of Termination II at Site U1475. Termination II (MIS 6/5 transition) at the studied site represents a major shift in both SST and productivity records at a regional scale (Figs. 2 3 4 5 ). It is characterised by the boundary between two long-term climate cycles at a global scale  55. Previous studies at a nearby location (MD02-2588) showed that U  K0  37 SST at the Agulhas Plateau reached its maximum temperature (~22 °C) for the entire 300 kyr interval during TII (Fig. 2b )  25. Our data indicates that TII marks the limit from a stratified water column to a progressive and continuous water column mixing, as seen from the F. profunda index (Fig. 4a ). Reconstructed primary productivity is also markedly affected by this transition and shifted from an in-phase pattern with glacial-interglacial variability (high during MIS 8 and MIS 6) to a total lack of congruence to glacial-interglacial cycles after TII (Fig.
4c, d ). Moreover, diatoms show much higher concentrations after TII (MIS 4 and 2) (Fig. 4g )  25  when the UPZ coccolithophore species started to continuously decline (Fig. 4f ). TII also represents a prominent change in the orbital periodicities of several palaeoenvironmental proxies (Supplementary Figs. 2  and 3 ). Productivity proxies (i. e. C 37:3-2 alkenones, coccoliths) show marked eccentricity frequencies (100 kyrs) preceding TII, but the cyclicity in the data either disappeared or attenuated after this period. In addition, the Ca/Fe ratio (Fig. 4b ), a proxy associated with marine carbonate production versus fluvial input in many circum-African margins  56, 57  and South African marine basins  58  , is only sensitive to obliquity cycle after TII (Supplementary Fig. 3c ). TII marks a step-change in water column conditions and forcing, from an eccentricity-dominated signal to a stronger obliquity influence over Site U1475.
The ~256-m-long splice at Site U1475 was scanned using a third generation Avaatech Core Scanner with a Canberra X-PIPS SDD, Model SXD 15C-150-500 150 eV resolution X-ray detector at the XRF Core Scanning Facility, IODP Gulf Coast Repository, College Station, Texas, USA. All core sections were scraped to clean the split core surface and covered with 4 µm -thick Ultralene plastic film (SPEX Centriprep, Inc. ) prior to scanning. Data were collected every 3 cm down-core in three separate runs using generator settings of 10 kV/0. 25 mA (no filter), 30 kV/1. 25 mA (Pd-filter) and 50 kV/1. 5 mA (Cu-filter), respectively. With the 10 kV setting, elements in the range from Al to Fe are detected, while at 30 kV, elements Rb, Sr and Zr are best resolved. Ba was measured with the 50 kV setting. For this study, we have only used the Ca and Fe data.
The Trace 1310 GC was equipped with a Rtx-5 column (60 m × 0. 25 mm × 0. 25 µm) using a temperature programme that started at 70 °C (1 min hold), then a temperature ramp of 20 °C per minute to 130 °C, followed by 4 °C per minute ramp to 320 °C, where it was held for 20 min. C 37:3-2 MARs were calculated using Eq. (  1 ). The dry bulk density (DBD) data was derived from shipboard measurements of gamma ray attenuation, which has been cleaned and corrected  67. MARs ¼ C 37:3À2 alkenone sedimentation rate DBD ð1Þ The unsaturation index U K0 37 was calculated using Eq. (  2 )  68  : U K0 37 ¼ C 37:2 C 37:2 þ C 37:3 ð2Þ Subsequently, SSTs were determined using the core top calibration following Eq. (3)  17  , which spans the temperature range of 0 to 27 °C and has a calibration error of ±1. 5 °C.