dataesr/scientific-paragraphs-categorization huggingface dataset:
For P8 cerebella, the 4 layers were sampled (i. e. IGL, PL, ML, and EGL), for P21 cerebella, the 3 remaining layers were cut (i. e. GL, PL and ML) with a laser microdissector (LMD 7000, Leica). For each cerebellar layer and each age, 0. 4 mm 2 of tissue was collected. RNA was extracted with the NucleoSpin RNA XS kit (Macherey Nagel), and then reverse transcribed and amplified with the SMARTer Pico PCR cDNA kit (Clontech, Kusatsu, Japan). To ensure that tissue from each cerebellar layer had been properly collected without any cross contamination, control real-time PCR experiments were performed with 8 different sets of primers, which amplify 2 genes specifically expressed in each of the 4 cerebellar cortex layers (Table  I ). These genes were chosen from the literature, the Brain Transcriptome Database (http:// www.
cdtdb. neuroinf. jp/CDT/Top. jsp) or the Allen Brain Atlas (http:// mouse. brain-map. org/). Stathmin 1 (Stmn1; Allen Brain Atlas, experiment 68632984) and atonal bHLH transcription factor 1 (Atoh1; Brain Transcriptome Database, CD03233) genes were selected as markers of the EGL. Calcium-dependent secretion activator 2 (Cadps2; 23) and tenascin R (Tnr; Brain Transcriptome Database CD01342) genes were selected as markers of the ML. Cholecystokinin (CCK; 24) and SDF-1 receptor (CXCR4; 25) genes were selected as markers of PL. Homer scaffolding protein 1 (homer1; Brain Transcriptome Database CD03205) and neurogenic differentiation 1 (Neurod1; Allen Brain Atlas experiment 75650865) genes were selected as makers of the IGL at P8 and GL at P21. As expected, Atoh1 and Stmn1 were significantly over expressed (ϩ83.
6% Ϯ 43. 6% and ϩ329. 8% Ϯ 22. 5%, respectively), when compared with the EGL at P8 (supplemental Fig. S4 ) and in the GL at P21 (ϩ377. 1% Ϯ 30. 2% and ϩ459. 1% Ϯ 34. 3%, respectively), when compared with the EGL at P8 (supplemental Fig. S4 ). Quantitative PCR-Two ng complementary DNA (cDNA) was amplified in the presence of 2 X SYBR Green Mastermix (Applied Biosystems) containing preset concentrations of dNTPs, MgCl 2 as well as forward and reverse primers, with a QuantStudio™ 12KFlex (Ap-plied Biosystems™). Proper controls without reverse transcriptase or with H 2 O instead of cDNA were conducted. Primers targeting nociceptin (Pnoc) and its receptor (Oprl1) were designed using the Primer Express software (Applied Biosystems) and validated by real-time PCR (Table  I ). The relative amount of cDNA in each sample was determined using the comparative quantification cycle (Cq) method and expressed as 2 Ϫ⌬⌬Cq using glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which was constant whatever the stage of cerebellar cortex development, as an internal standard for variations in amounts of input mRNA.
To examine gene expression levels of nociceptin and its receptor in CGN and cultured astrocytes, 4 biological replicates and 3 technical replicates (i. e. a total of 12 samples per day of culture) were analyzed. To study the effect of nociceptin on cultured granule neurons, 4 parameters were analyzed, i. e. cellular caspase activity, survival, motility and differentiation. For cell survival Results from each image were the average measurement from at least 28 cells, (i. e. over 700 cells were measured per condition). Statistical analysis was performed with GraphPad Prism® (version 6. 04). Normality was tested with a Shapiro-Wilk test; when the data were parametric an ANOVA was used, when not a Kruskal-Wallis was used instead. Statistically significant differences were estimated by ANOVA followed by Bonferroni's tests for measurement of cell survival, motility and differentiation, and with Kruskal-Wallis followed by Dunn's tests for differentially expressed peptides, qPCR and caspase experiments and with a Mann-Whitney test for the targeted MS/MS.
RESULTS Identification and Quantification of Peptides Within the Rat Cerebellum-The peptides expressed in the cerebellum during development were characterized by mass spectrometry and identified by means of a database containing 184 rat neuropeptides or neuropeptide precursors (supplemental Table  S1 ). To confirm the reproducibility of the extraction protocol and mass spectrometry analysis, HSA level in the four groups was measured as an external standard and no significant difference was found (supplemental Fig. S5 ). Analysis with SpectrumMill and Mascot software packages revealed 33 peptides expressed in at least 7 out of 10 samples, at one or several stages of development (supplemental Table  S2 ). Quantification of peptide relative expression level with Progenesis software showed that 8 peptides were differentially expressed between 2 or more developmental stages (Table  II ).
Nevertheless, this was only a transient increase as, by P21, NOP mRNA level subsequently decreased compared with P16 and remained low at adulthood. Laser microdissection of the different cerebellar cortex layers revealed that, at P8 (Fig. 4 ), nociceptin mRNA was mainly expressed in the IGL and appeared significantly less abundant in the EGL, ML, and PL. In the same experiments, NOP mRNA was only expressed at P8 in the IGL/GL with no detectable expression in the other layers (data not shown). Because the IGL is mainly composed of CGN and astrocytes, real time PCR was performed on these two types of cells in primary cultures to measure gene expression of the nociceptin and its receptor. Cultured CGN exhibited strong expression of nociceptin gene with a gradual decrease until culture day 5 (supplemental Fig.
5C ). Similar results were observed when cells were treated with nociceptin and/or H 2 O 2 , 24 h after plating (data not shown). To investigate the possible effect of nociceptin on granule neuron migration during development, cell motility was measured. Microexplants from P8 cerebella were cultured for 24 h and then treated with nociceptin. In control conditions, granule neurons moved regularly from their origin toward the outside of the microexplant during the whole recording period (Fig. 6A ) at an average speed of 344 m/h (Fig. 6B ). Addition of nociceptin (10 Ϫ8 M) after 45 min of recording did not affect CGN motility (Fig. 6B ) while, as expected, addition of PACAP (10 Ϫ7 M) as a positive control decreased CGN motility (Fig. 6B ). To examine the possible effect of nociceptin on CGN differentiation, cultured cells were treated for 24 h with nociceptin in the presence or absence of H 2 O 2 (Fig.
Tissues were heat-denatured immediately after sampling to prevent degradation by proteases, and peptides were purified by filtering the tissue extract with a 10-kDa cutoff filter to eliminate heavy proteins. Analysis of the MS/MS data from all the samples with the SwissProt Rat database identified less than 100 proteins with only half of them reproducibly found in the cerebellum, showing the robustness of the peptide extraction procedure used. These proteins represent less than 1% of the entries of the database, indicating that the extraction protocol excluded virtually all proteins from the samples, and retained almost only peptides known to be expressed at low level compared with highly expressed proteins such as tubulin. Indeed, the present extraction protocol was chosen after optimization and comparison of several operating procedures.
Nevertheless, the fact that a few proteins were also retained suggests that, despite all experimental precautions, some minor degradation still occurred in the time between tissue sampling and mass spectrometry analysis. It would thus be of interest to test additional extraction methods in which for instance tissues are immediately frozen in 2-methyl-butane  (29)  or peptides are directly extracted upon sampling  (30). One of these approaches may reduce further sample contamination by protein fragments and improve the analysis of peptides present in the tissues. However, the protein fragments identified may also arise from the physiological turnover induced by enzymatic proteolysis through ubiquitin or proteasome pathways  (31). Peptide identification was conducted by means of a rat database which includes 184 sequences of known active peptides and peptide precursors.
A size limit was set to 100 amino acids for peptides to be included in our database. Sequences encompassing over 100 amino acids, such as brain-derived neurotrophic factor or neurotrophin-3 (both 119 amino acid long) were excluded even though nLC-MS analysis revealed their presence in the cerebellum, in agreement with previous studies  (32). From the 184 sequences present in the database, 70 peptides were identified in at least 1 of the 10 samples, at one or several stages. Nevertheless, to ascertain a reproducible presence, only 33 peptides found to be expressed in at least 7 out of 10 samples at one or several stages of development, were considered for further analysis. These 33 peptides represent almost 18% of all the entries of the database, indicating that a large diversity of peptides is expressed in the cerebellum.
As a matter of fact PACAP is only expressed by Purkinje cells in the developing cerebellum  (35)  and thus its abundance in the whole cerebellum remains very low. As whole cerebella were analyzed, despite our enrichment procedure, the samples remained very complex yielding to the collection of a huge number of peptide sequences (around 1400 per stage) and, consequently, low abundant peptides may have been hidden by other molecular species and not selected for fragmentation. This hypothesis is supported by the fact that although PACAP was not detected, the PACAP-related peptide, which originates from the same precursor, was found  (36). It should also be pointed out that, as the analysis was conducted using a specific database containing only known neuropeptides and peptide precursors, we were unable to identify peptides com-ing from unknown precursors or from precursors not included in the database.
Mean stress effect In order to study the mean stress influence, the data from specimen D are analysed because it offers the most diversified load ratio results; R=-0. 2, -1, -2 with relieved residual stress and R=-1 without relieved residual stress. The S/N curve slope for no stress relieved specimen is m=4, for stress relieved specimen m=5. For each load ratio category an S/N curve is established and a 2 000 000 cycles stress amplitude is evaluated and given in Tab. 2.
Measurements of light -optical attenuation Instruments at HBAO operate from a roof terrace at approximately 30 m above the ground. The terrace hosts the sampling inlets, from which air is drawn into a laboratory room located underneath by straight stainless-steel pipes to avoid particle losses. The optical attenuation of light (ATN) by aerosol particles smaller than 1 µm in aerodynamic diameter was measured by a single-wavelength aethalometer (model AE-14U, Magee Sci. , Berkeley, CA, USA) operating at 880 nm and sampling at 3. 5 (±0. 1) L min -1 from a certified PM 1 inlet (BGI Inc. , Waltham, MA). The physical principle of operation of the aethalometer is detailed in  Hansen et al. (1984). Measurements were performed at a 5 min time resolution and stored on a data logger (model CR-1000, Campbell Sci.
Ltd. ). The original dataset was screened to eliminate spikes and peaks lasting less than 2 h, gener- The Lambert-Beer law relates the temporal variation in the measured light attenuation (ATN) due to aerosol particles collected on a quartz fibre tape to the mass concentration of eBC (in µg m -3 ). This is based on the fact that BC is the strongest light absorber in the near-infrared  (Kirchstetter et al. , 2004; Caponi et al. , 2017). The operational equation linking eBC to the attenuation (ATN) measured by the aethalometer is eBC = 1 MAC BC 1 C • R(ATN) A V ATN t , (1) where A represents the area of the aerosol deposited on the filter, V the volumetric flow rate and ATN/ t is the variation rate of attenuation with time. The terms C and R(ATN) account for measurement artefacts that artificially increase absorption estimated from attenuation measurements.
Supporting data In 2013, the mass concentration of particles of diameters smaller than 2. 5 µm in equivalent aerodynamic diameter (PM 2. 5 ) was sampled by a tapering element oscillating microbalance (TEOM, model 1400a, Rupprecht and Patashnick, Albany, NY, USA) operating from a certified PM 2. 5 inlet (also from Rupprecht and Patashnick). The total flow rate at the inlet was 16. 7 L min -1 to ensure the correct functioning of the inlet, and the sampling flow rate driving the aerosol-laden air to the microbalance was 3 L min -1. The temperature of the sample stream was kept constant at 50 • C. Three-dimensional air mass back-trajectories are calculated using the NOAA HYbrid Single-Particle Lagrangian Integrated Trajectory Model (HYSPLIT;  Draxler and Rolph, 2015). The model uses the 1 • ×1 • latitude-longitude grid reanalysis meteorological database.
The 6 h reanalysis archive data are generated by the NCEP's GDAS (NCEP: National Centers for Environmental Prediction; GDAS: Global Data Assimilation System) wind field reanalysis. Further information can be found at https://rda. ucar. edu/datasets/ds083. 2/ (last access: 12 November 2018). ERA-Interim reanalysis data  (Dee et al. , 2011)  from the European Center for Medium Range Weather Forecasts (ECMWF) are used in the analysis of synoptic scale circulation patterns associated with the identified dominant air mass transport to Henties Bay. The 6-hourly (00:00, 06:00, 12:00, 18:00 UTC) analysis data (0. 75 • × 0. 75 • ) at mean sea level pressure (MSLP -variable 151. 128) and the 500 hPa geopotential height (ZG500 -variable 129. 128) are used for this study. Datasets were normalised (MSLP/100 and ZG500/100) using Climate Data Operators (CDO)  (Schulzweida et al.
, 2006)  and plotted with 2 and 10 hPa isobaric intervals for MSLP and the 500 hPa level, respectively. Surface BC concentrations predicted by the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2; Gelaro et al. , 2017) sampled at HBAO and at a number of other sites  (Zuidema et al. , 2016)  are used for comparison. The HTAP_V2 dataset is used for gridded emission of anthropogenic BC for the year 2010  (Janssens-Maenhout et al. , 2015). It consists of 0. 1 • × 0. 1 • grid maps. HTAP_V2 uses nationally reported emissions combined with regional scientific inventories in the format of sector-specific grid maps. The grid maps are complemented with EDGARv4. 3 data for those regions where data are absent. Anthropogenic activities producing BC aerosols comprise aviation, transportation, energy production, industries, ship traffic, residential and agricultural burning.
This points to the inherent degree of uncertainty in our estimates. The correction factors (filter loading and multiple scattering corrections) needed to convert the measured attenuation into a eBC concentration value are assumed and not evaluated from concurrent measurements, and set to fixed values as the aerosol at HBAO would derive from a single source type. We do not deal with potential changes in the aerosol properties due to ageing. Differences could also be due to the representation of the timing and extent of a southward shift of the easterly wind during summer. Although these issues cannot be resolved with the present dataset, they question the representation of the transport of smoke plumes at the subcontinental scale of southern Africa. There is no doubt that the transport of wildfire smoke is the major regional source of the eBC aerosols for the western coast of Namibia.
5 (±0. 5) µ g m -3. For comparison, the mean PM 2. 5 mass concentration at HBAO was 14 (±11) µ g m -3 in 2013 (Fig. S1 ). These aerosols below clouds would have a negligible direct radiative effect. There are almost no AERONET measurements of the aerosol optical depth (AOD) at HBAO concurrent to the eBC data series. However, Fig. S2  shows the time series of the AERONET level 2. 0 AOD of the fine and coarse mode aerosols (AOD F and AOD C ) evaluated by the O'  Neill et al. (2003)  algorithm between December 2011 and May 2012, and then from May to December 2015. Figure  S2  shows that the AOD F varies significantly from background values in the December 2011-May 2012 period (average 0. 05 ± 0. 03) to peak values of 0. 4 and higher during August, September and October 2015, when the transport of biomass burning occurs in the free troposphere  (Swap et al.
260888) as well as by the Partenariats Hubert Curien (PHC) PROTEA of the French Ministry of Foreigns Affairs and International Development (contract numbers 33913SF and 38255ZE). We acknowledge the use of the HYSPLIT model from the NOAA Air Resources Laboratory (ARL), the use of FIRMS data and imagery from the Land Atmosphere Near-real time Capability for EOS (LANCE) system operated by the NASA/GSFC/Earth Science Data and Information System (ESDIS) with funding provided by NASA/HQ, the archiving and distribution of the HTAPv2 grid map by the Emissions of atmospheric Compounds and Compilation of Ancillary Data (ECCAD) database. The global grid maps are a joint effort from US-EPA, the MICS-Asia group, EMEP/TNO, the REAS and the EDGAR group to serve in the first place the scientific community for hemispheric transport of air pollution.
The static version is available on this EDGAR website, but also the GEIA data portal and the ECCAD server. ECCAD is the GEIA Global Emission InitiAtive database (http://www. geiacenter. org/, last access: 12 November 2018) and is part of AERIS, the French data service for Atmosphere (http://www. aeris-data. fr/, last access: 12 November 2018). MERRA-2 data are available at MDISC, managed by the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC). Thanks are due to A. Da Silva (NASA/Goddard Space Flight Center, Global Modeling and Assimilation Office, Greenbelt, MD, USA) for making the extractions at HBAO available. Edited by: Andreas Petzold Reviewed by: three anonymous referees.
Genetic architecture of EWS. Our new, expanded GWAS of Ewing sarcoma has identified three new loci and also validated the three previously reported susceptibility regions. In analyses of the new loci, there is evidence of informative eQTLs with nearby biologically plausible candidate genes that could be likely target genes for future functional investigations. Additionally, EWSR1-FLI1 ChIP-seq data suggest evidence for potential interactions of germline variation at the 6p25. 1 and 20p11. 22 loci with the EWSR1-FLI1 fusion protein as recently discovered at the 10q21 locus  23. It is remarkable that six independent susceptibility regions with relatively large effect sizes (estimated OR > 1. 7) have been discovered in a sample of 733 EWS cases. These results provide a strong contrast to GWAS findings for the vast majority of cancers that report estimated effect sizes less than 1.
Methods Study populations. EWS cases and controls for this GWAS originated from several contributing studies. A set of published French EWS cases (N = 401) and ancestry matched controls (N = 682) was extracted from the previously published GWAS on EWS  22. In addition, we combined a set of 122 French EWS cases from the Institut Curie, 19 EWS cases from the National Cancer Institute (NCI) Center for Cancer Research (CCR), 29 EWS cases from the NCI Bone Disease and Injury Study  33  along with 162 EWS cases from the Childhood Cancer Survivor Study (CCSS)  34, 35. The SNPWEIGHTS software was used to calculate the percentage of European ancestry using a set of population inference SNPs  36, 37. Only EWS cases with >80% genetically estimated European ancestry were included in the analysis. This resulted in a total of 749 EWS cases combined with 682 cancer-free controls from the original EWS GWAS.
The first three principal components were used as matching factors and a 2:1 matching ratio of controls to cases was carried out based on the availability of close control matches. Matching was performed first for the CCSS set to maximize matches with available controls on high-density arrays. In total, our final analysis set contained 733 EWS cases and 1346 cancer-free controls. All EWS cases were confirmed by medical record review and the presence of a specific EWSR1-ETS translocation were noted when data was available. Adult controls were of European ancestry and cancer-free at time of DNA collection. Each participant provided informed consent and each participating study was approved by the Institutional Review Boards of their study center. Genome-wide SNP genotyping and quality control assessment.
1), rs7832583 (8q24. 23), rs12106193 (20p11. 23) and rs6106336 (20p11. 23). Standard protocols were followed according to manufacturer's guidelines when performing the TaqMan assays (Supplementary Table  7 ). Assays were first tested on HapMap samples to ensure validity before testing on EWS cases and controls included in the GWAS. 7 ). Standard manufacturer's protocols were followed when performing allelespecific PCRs with these TaqMan assays. The 3502 German controls from the KORA S4 cohort were genotyped with the Affymetrix Axiom array and imputed using the 1000 Genomes phase 3 as well as the Haplotype Reference Consortium (HRC) reference panels. EWS functional data. All expression quantitative trait loci (eQTL) analyses were performed using previously published expression data from 117 EWS samples  22.
Samples were profiled using Affymetrix Human Genome U133 Plus 2. 0 gene expression arrays. Expression data are publically available at the Gene Expression Omnibus (GEO) web portal (GSE34620). Affymetrix expression data were normalized with the NormalizeBetweenArrays function of the LIMMA package (http://web. mit. edu/~r/current/arch/i386_linux26/lib/R/library/limma/html/ normalizebetweenarrays. html). Wald tests of estimated betas from linear regression models were performed to asses for allele specific differences in gene expression levels. Chromatin immunoprecipitation (ChIP). ChIP experiments were performed following manufacture instructions using iDeal ChIP-seq kit for transcription factors and for histones (Diagenode) with respectively a rabbit polyclonal anti-FLI1 antibody (Ab15289, Abcam) and a rabbit polyclonal anti-H3K27ac (Ab4729, Abcam).
Reads were aligned to hg19 reference genome with Bowtie2 42. Peaks were called with MACS2  43  with the option narrow for FLI1 ChIP-seq and broad for H3K27ac ChIP-seq. For each cell line, ChIP-seq results were normalized according to their input sample. Comparison of gene expression levels across cancer types. Publicly available gene expression data for 19 different cancer entities comprising in total 616 tumor samples, which were all profiled on Affymetrix Human Genome U133 Plus 2. 0 gene expression arrays, were downloaded from the GEO or the Array Express platform of the European Bioinformatics Institute (EBI) (accession codes: GSE68015, GSE13433, GSE32569, GSE19404, GSE35493, GSE58697, GSE34620, GSE34800, GSE60740, GSE19348, GSE17743, GSE8167, GSE53224, GSE16476, E-MEXP-3628, GSE14827, GSE33458, E-TABM-1202, GSE29683, GSE20196, GSE21050).
Microarray data were simultaneously normalized using Robust Multi-Chip Average (RMA)  44  using brainarray CDF (v19 ENTREZG) yielding one optimized probe-set per gene  45. Analysis of EWSR1-FLI1-modulated genes in vivo. For transcriptome-wide analysis of EWSR1-FLI1-modulated genes 5 × 10 6 A673/TR/shEF1 cells  46  , which contain a doxycycline (dox)-inducible shRNA against EWSR1-FLI1, were injected subcutaneously in the flanks of immunocompromised NSG (Nod scid gamma) mice. A673/TR/shEF1 cells were authenticated by STR-profiling to match their parental A673 cell line and were routinely tested for mycoplasma contamination by PCR. When tumors reached an average volume of 180 mm 3 , mice were randomized and either received 2 mg/l dox (Sigma) and 5% sucrose in the drinking water (dox+) or only 5% sucrose (dox -).