dataesr/scientific-paragraphs-categorization huggingface dataset:
We first performed RNA fluorescence in situ hybridization (FISH) experiments in wildtype embryos to detect nascent transcripts of eight Drosophila Hox genes, using probes recognizing the first introns of those genes. As expected, our results show sequential expression of lab, pb, Dfd, Scr, Antp, Ubx, abdA and AbdB along the anteroposterior axis  [21, 26]  at the germ band elongated stage (3:50-7:20 after fertilization) (Extended Data Fig. 1a-f ), which is conserved throughout Drosophila embryogenesis (Extended Data Fig. 2 ). We then performed a series of immuno-DNA FISH experiments in embryos at the germ band elongated stage to address 3D chromatin compaction of Hox clusters. We measured 3D distances between FISH spots for Ubx, abdA and AbdB of the BX-C cluster or lab, Scr and Antp of the ANT-C cluster.
Acknowledgements We thank  Montpellier Resources Imaging  facility  MRI-IGH  for microscopy support. We thank  Satish Sati  and  Frédéric Bantignies  for critical reading of the manuscript. G. C. Research in the laboratory of G. C. was supported by grants from the  European Research Council  ( ERC-2008-AdG No 232947 ), the  CNRS , the  FP7 European Network of Excellence EpiGeneSys , the  European Union 's  Horizon 2020 research and innovation programme  under grant agreement No  676556  (MuG), the  Agence Nationale de la Recherche , the  Fondation pour la Recherche Médicale , INSERM, the  French National Cancer Institute (INCa)  and the  Laboratory of Excellence EpiGenMed.
Vertical water entry of a flat panel In this first section the vertical impact of a flat plate is numerically investigated and validated. Specifically, results of the 2D single-phase simulations are described and compared to the experimental data from a wet drop test performed in  [9]. In that work a flat panel (panel length L equal to 64 cm) impacting with a deadrise angle of 4° and a vertical impact velocity U of 6. 0 m/s is studied. Measures of pressures at several positions along the plate are taken, allowing for a detailed control of the pressure peak repeatability and for possible 3D effects. As described in the theoretical work by  [10] , for these small deadrise angles a very thin, high-speed jet of water is formed, and the time-spatial gradients of the pressure field are extremely high.
Having in mind such limits, through SPH it is possible to get predictions close to the experimental data if the pressures are integrated over the experimental gauge area, even when using a speed of sound c 0 smaller than the real one  0 *. In figure  7  the experimental pressure time histories recorded on a sequence of pressure probes is reported. Even if the experimental pressure peaks present some fluctuations, very similar pressure evolutions are recorded with an almost constant time shift at each probe. The SPH results show quite good repeatability of the pressure peaks along the wedge surface as well (see figure  8 ). In this regard, it is worth comparing the propagation velocity of the pressure peak along the plate, U P. Indeed, in water entry flows the value of the pressure peak should correlate to U P 2 (see e.
Description of the experimental data Guided ditching impact experiments  [19] ,  [23]  were performed in the CNR-INSEAN towing tank, which is 470 m long, 13. 5 m wide and 6. 5 m deep. The dimension of the flat plate were 500 mm by 1000 mm (fig. 13 ). Pressures at 18 points are measured through Kulite XTL123B pressure transducers. The sampling rate of the latter is 200 kHz while their dimension is 3. 8 mm. The horizontal and vertical velocities at the impact are respectively 40 m/s and -1. 5 m/s. In the experiments, these velocities are assumed to remain constant during the whole ditching impact.
Subjects From 2010 to 2016, patients were included at the Department of Clinical Nutrition (University Medical Center, Rouen, France). Patients were included if they were aged above 18 years, without acute diseases, followed for malnutrition, obesity, or eating disorder. After an overnight fasting period of 12h, weight and height were measured by the same operator dressed light clothes without shoes. BMI was calculated as body weight (kg) divided by squared height (m 2 ). The study was approved by the Local Ethics Committee for Non-Interventional Studies (CERNI, Comited'Ethique pour la Recherche non interventionnelle) and all data were fully anonymized.
Dual-energy X-ray absorptiometry (DXA) DXA was performed on the whole body using a Lunar Prodigy Advance (General Electric Healthcare) without specific preparation. The assessment of QA and QC data for the DXA measurements was done every morning when patient assessment was planned and at least 3 days per week. The QA and QC data were sent each month to an independent security and control society for monitoring. Over the 6-year period, no deviation was observed and there was no firmware or software upgrades. The manufacturer controlled the DXA equipment at least one time per year. During measurement, all patients had their underwear on and no metal accessories worn. DXA uses an X-ray generating source, with two X-ray beams with different energy levels. Based on their X-ray attenuation properties, FFM (lean mass and bone mineral content) and FM were measured.
20) (21)  Curative therapy of childhood HCC requires complete surgical resection. In nonresectable tumors, liver transplantation (LT) may be considered. (4) Although several case series indicated a favorable outcome of LT in childhood HCC,  (22) (23) (24) (25)  there are no studies available comparing survival rates of pediatric and adult HCC patients taking into account the underlying cause of HCC. A systematic assessment of the outcome of children who underwent LT for HCC was reported in 2006 for the United Network for Organ Sharing (UNOS) database  (26)  and updated to an extended cohort  (27)  in 2010 showing a 5year patient survival rate of 53. 5%. In this study, however, no information on underlying disease was reported so that HCCs based on inherited liver disease and acquired noninherited liver disease could not be differentiated.
ELTR DATABASE Established in 1985, the ELTR is a voluntary collaboration of 168 European Liver Transplant Centers in 31 countries. (28) For ELTR, a prespecified set of variables is collected for each LT patient in the participating centers after transplantation. Moreover, follow-up data are provided by contributing centers at each follow-up visit so that retransplantations as well as deaths can be recorded. All data are monitored by ELTR staff at regular intervals. Quality of the data is controlled by annual site visits at randomly chosen participating centers. (29) Coverage of LT patients in Europe within ELTR has been shown to be as high as 97% in 2012. Data obtained from the ELTR database can thus be described as highly representative for Europe. None of the participating centers' donor organs were at any point obtained from executed prisoners or other institutionalized persons.
STUDY DESIGN AND ANALYSIS PLAN We conducted a historical cohort study based on prospectively collected data from ELTR. In order to investigate the main hypotheses of this study, a 3-stage data analysis plan was developed. This was necessary as age at transplantation and underlying liver disease causing HCC are highly collinear to each other and are difficult to separate in an overall analysis, so that stratified analyses needed to be performed. In a first step, PinHCC patients were compared with pHCC patients to investigate if there was a difference in survival rates between these 2 types of HCC in childhood. Because the underlying cause of LT in the group of pediatric patients without inherited diagnosis was often missing or unspecific, we performed a sensitivity analysis comparing PinHCC with pHCC patients with a definite noninherited cause of HCC only (n 5 18; Table  1 ).
Data Management and Statistical Analyses The data set extracted for this study was checked for plausibility by ELTR staff and by the authors of this manuscript. In case of implausible or missing data (eg, unspecified cause of transplantation), the transplant center was recontacted by ELTR staff (V. K. ). Missing data were obtained as far as possible, and errors were corrected accordingly. Follow-up for each individual included the time from first LT to last recorded visit at the transplant center or death. Patient survival was defined as the time between first LT and death. Graft survival was defined as the time from first LT to retransplantation or death (whatever happened first). Censoring due to being lost to follow-up for the transplant center was assumed to happen completely at random.
All data analyses were performed using Stata, version 12 (StataCorp, College Station, TX). Baseline characteristics were compared between groups using chi-square tests, Fisher's exact tests, and Wilcoxon rank sum tests as appropriate. Survival times were displayed using Kaplan-Meier plots and were compared between groups using univariate and multivariate shared frailty Cox regression models (adjusted for sex, age, year of transplantation, and allowing for clustering of outcomes by transplantation center by using a shared frailty term). Proportional hazards assumptions were assessed using Schoenfeld residuals. In case of nonproportional hazards, piecewise regression models were used.
45) after adjusting for age so that inherited liver disease can be seen as an additional prognostic factor for better survival rates in pediatric HCC. A survival advantage based on associated inherited disease was not seen in adults, where HCC patients with and without inherited liver disease showed similar survival rates. This might be attributable to the different types of inherited liver diseases, which are associated with HCC in children and in adults (Fig. 1 ). This is the first study which assessed comprehensively the competing effect of pediatric HCC and underlying inherited liver disease on patient and graft survival after LT. Crude overall survival rates were thereby in line with the largest previously published patient cohort from the UNOS database. (27) Data on pediatric HCC patients undergoing LT are otherwise sparse.
Because of small numbers of patients with childhood HCC, there is little evidence regarding optimal treatment for this group of patients. Children with HCC are therefore evaluated for LT extrapolating experience from adult patients by applying the conventional Milan criteria. The criteria have been modified repeatedly, and these and other more liberal criteria like the University of California, San Francisco criteria have been a matter of ongoing debate. (30, 31) The ELTR data presented here provide the most comprehensive cohort of children who underwent liver transplantation for HCC. Our results suggest that prognosis of a child with underlying inherited liver disease is generally better than anticipated. However, our analyses and the underlying data set have several limitations. One major limitation is the lack of characterization of the individual HCC with respect to the histological and radiological stages and tumor volume.
M-S196A Induces Expression of FoxM1 and Lesion-Resident Cells. Examination of the RNA-seq datasets revealed LXRα-S196A cells expressed almost threefold (P = 7. 76E-14) more protooncogene FoxM1 compared with macrophages expressing WT LXRα (Fig. 3A  and SI Appendix, Fig. S4D ). This was also the case for several FoxM1 target genes (16) (Fig. 3A  and SI Appendix, Fig. S4D ). While LXRα activation was previously shown to inhibit cell proliferation via inhibition of FoxM1 in hepatic carcinoma cells  (17) , its regulation in macrophages has never been documented. LXRs modulate gene transcription by heterodimerizing with the retinoid X receptor (RXR) and binding to specific DNA sequences termed LXR response elements (LXREs) in the transcriptional regulatory regions of their target genes  (18). Similar to the wellknown Srebf1 LXR target (Fig.
S7D ). For instance, genes involved in nuclear division and cell cycle regulation remained strongly induced by LXRα-S196A, further emphasizing the importance of LXRα phosphorylation in the modulation of these pathways. Remarkably, it became apparent that while a small subset of genes was differentially regulated by the mutant only in the context of the ligand (94 induced and 50 reduced compared with WT cells), most differences in gene expression were observed in the absence of ligand (Fig. 5  A and B). Additionally, our datasets showed that ligand responses (either induction or repression) were similar in both WT-and mutant-expressing macrophages for a subset of genes, but not for others (Fig. 5C  and SI Appendix, Fig. S8 ). Further analysis revealed that both the magnitude of the response and the identity of the genes were strikingly different between the response to the ligand (regulation by GW in either WT or S196A cells) and to phosphorylation (modulation by LXRα-S196A compared with WT cells) (SI Appendix, Fig.
Overall, our findings further highlight the importance of this set of molecules in atherosclerosis progression. Importantly, we show evidence that reduced LXRα phosphorylation during atherosclerosis development reprograms the macrophage transcriptome (Fig. 2 ). Global gene expression analysis revealed that in these cells, most genes are sensitive to the expression of the LXRα phosphomutant in the absence of LXR ligand stimulation, with only an additional 82 genes being modulated by the mutant in the presence of the GW3965 ligand compared with the 670 LXRα phosphorylation-sensitive genes under basal conditions (SI Appendix, Fig. S7 E  and F ). This suggests that modulation by LXRα-S196A expression is different from the regulation by ligand activation of the receptor. Indeed, comparison of the various datasets evidenced that the transcriptomic rewiring in response to impaired LXRα phosphorylation in the mutant cells is remarkably distinct and does not merely phenocopy ligand responses (Fig.
ACKNOWLEDGMENTS. We thank  Prof. Edward Fisher  and  Prof. Michael Garabedian  ( New York University School of Medicine ) for their insightful discussions and  Theresa Leon  for providing Jurkat cells. This work was supported by  Medical Research Council New Investigator  Grant  G0801278  (to I. P. -T. ), British Heart Foundation (BHF)  Project Grant  PG/13/10/30000  (to I. P. -T. ), a  University College of London Grand Challenges PhD Studentship  (to I. P. -T. ),  BHF  Studentship  FS/12/59/30649  (to I. P. -T. ), the  Royal Free Charity PhD Program in Medicine (I. P. -T. ) , and the  University College London Division of Medicine  (I. P. -T. ). It was also supported by  Spanish Ministry of Economy and Competitiveness  Grants  SAF2014-56819-R  (to A. C. ) and  SAF2015-71878-REDT  (to A. C.
Patients characteristics and sampling Biobanking and testing of biological materials were approved by the Central Ethical Review Board of the Italian National Cancer Institutes (CEC/707/15 dated 13 October 2015), and were conducted in compliance with the World Medical Association Declaration of Helsinki. Each participant signed a written informed consent authorizing the collection of genomic information (except germline, genome-wide data) from both tissues and blood, as well as anonymized data exchange/ dissemination exclusively for scientific, nonprofit purposes. The clinical characteristics of the patients are presented in Table  1. Tumor tissue specimens were collected on the occasion of either surgery or diagnostic excisional biopsy. Upon histologic examination, all cases showed a typical ES phenotype with a small blue round cell morphology, an immunohistochemical intense membranous stain for CD99, nuclear positivity for FLI1, occasional staining for synaptophysin, and no detectable muscular, cytokeratin and lymphoid markers.
As to dPCR, matched tissue RNA and ctRNA from each patient were always run in parallel to insure consistency. dPCR reactions were set up in a final volume of 16 μl including 8 μl of 2x Master Mix, 0. 9 nM each of forward and reverse primers, 0. 25 nM of TaqMan ® MGB probe, and 7. 0 μl of template. The mix was loaded onto dPCR chips, and thermal cycling was as follows: an initial denaturation step of 10 min at 96. 0°C, then 39 cycles for 2 min at 58. 0°C and 30 sec at 98. 0°C, followed by a final elongation step of 2 min at 60°C. Threshold values (positive versus negative; blue versus yellow spots) were automatically calculated by the ThermoFisher Cloud Analysis Suite in tissue RNA from each patient, manually reviewed, and then applied to ctRNA assays from the same patient with no additional data manipulation.
Correlation between metabolic tumor uptake and ctRNA burden Finally, we looked for possible correlations between conventional volumetric PET parameters on the one hand, and copy numbers of EWS fusion transcripts in blood, on the other. MTV and TLG values were calculated by two different thresholds (SUV = 2 and 40% of SUV max ), and were paired with copy numbers of EWS transcripts, estimated by dPCR at each of the five time points for which both sets of data were available in four patients. High (>0. 85) and statistically significant (p < 0. 05) regression coefficients were obtained for MTV 2 , MTV 40% and TLG 40% , whereas a nonsignificant correlation trend was obtained for TLG 2 (Supplemental Figure  S1 ). Thus, the available data, although limited, suggest a functional link between PET volumetric parameters and the release of driver oncogenic fusions into the bloodstream.
Field-emission scanning electron microscopy (FE-SEM) 60-µm-thin sections were coated with chromium in a sputter coater and examined with a JEOL 6700F fieldemission scanning electron microscope using an accelerating voltage of 5 kV. High-magnification images were analysed using the ImageJ software (http://image j. nih. gov/ij/) to determine the Feret diameter of the observed fibrillary structure. Ten fibrils were measured on two different images for each sample by manually applying a circular area covering the fibrils and values were averaged for comparison.
Data and statistical analysis Wet chemical analysis experiments were carried out in triplicate, and the results are expressed as mean ± standard deviation. An analysis of variance (ANOVA) was performed on the obtained values followed by a Tukey test for comparison with the corresponding untreated samples with a significance level of probability set at p < 0. 05. Statistical analyses were performed using the SigmaPlot 12. 0 software (Systat Software, Chicago, USA).
Acknowledgements The authors would like to thank some members of the  FARE  staff:  David Crônier  for his help in performing chemical and 2D HSQC NMR analyses,  François Gaudard  for his help in performing the SEM observations and  Olivier Delfosse  for conducting the catalytic combustion experiments. Finally, the authors are grateful to  Dr Lloyd Donaldson  ( SCION, Rotorua, New-Zealand ) for his help in acquiring the FE-SEM images.
2010a; Zhang et al. 2012a; Orro et al. 2015) , broad substrate specificity and genome plasticity  (Larkin et al. 2010b). In turn, the alkaneoxidizing capabilities of rhodococci are considered permanent and typical traits since in most of the strains the alkB gene is predominant  (Nie et al. 2014 ) and it occurs in multiple copies  (Zhang et al. 2012a; Orro et al. 2015 ; Table  3 ). On the other hand, only one copy of chromosomally encoded alkB was identified in the R. opacus R7 genome sequence  (Orro et al. 2015). However, a great number of genes coding for putative P450 monooxygenases were shown in this strain, and these enzymes may also be involved in alkane metabolism  (Orro et al. 2015). Based on the recently available information regarding genome sequences of Rhodococcus opacus (9 sequences have been deposited in the NCBI GenBank until April 2018) it is apparent that particular strains of this species may possess different numbers of the alkB gene copies.
The first characterized fluoranthene-degrading strain, C. indicus P73 T , also transformed other lower PAHs such as naphthalene and phenanthrene  (Cao et al. 2015). Its alkane conversion abilities were not studied; however, a closer look at the bioinformatic data deposited in NCBI GenBank enabled us to identify the alkB genes in the genome sequence of P73 T. This finding suggests that the strain may utilize saturated aliphatic hydrocarbons besides aromatic compounds. The metabolism of an n-alkane and phenanthrene was reported for the strain representing the genus Stappia (Rhodobacteraceae family;  Al-Awadhi et al. 2007 ). This bacterium utilized both compounds at halophilic conditions (3. 5% NaCl). Rodrigues et al. (2015) , in turn, found the enhanced degradative potential among Tristella genus (Rhodospirillaceae family).
Bacterial cultures were incubated with crude oil, and proteomes as well as degradation of n-alkanes and PAHs were analyzed over time. Such an integrated methodology led to observations of the crude oil impact on the regulation of bacterial enzymes responsible for PAH degradation. This review presents the currently available data regarding degradation capabilities of both n-alkanes and aromatic hydrocarbons. However, the reader should be aware of the fact that the quality of the collected information varies strongly depending on the source and date of publication as well as experimental setup applied. The methodological reliability should be particularly concerned since there are many different techniques used to evaluate the microbial catabolism of hydrocarbons (see above). For some well-characterized and thoroughly studied hydrocarbon degraders (such as Mycobacterium vanbaalenii PYR-1), there is considerable and widespread empirical evidence (genetic, genomic, proteomic) indicating catabolic preferences and elucidating metabolic pathways.
Acknowledgements We would like to thank  Dr. Piotr Kapusta  ( Department of Microbiology, Oil and Gas Institute-National Research Institute, Poland ) for his advice and help during the preparation of this manuscript. The work was financially supported by the research grant of the  Polish National Science Centre  No. UMO-2012/07/N/NZ9/00920. Open Access This article is distributed under the terms of the Creative Commons Attribution 4. 0 International License (http:// creativecommons. org/licenses/by/4. 0/),which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
2009; Goff et al. 2011a; Williams et al. 2013). The growing body of interdisciplinary evidence for an event around the midfifteenth century means that region-specific archaeological proxies such as region-wide coastal village abandonment, oral traditions, anomalous coral sand/pumice layers and reworked sand dunes  (Goff et al. 2008a (Goff et al. , 2011a) )  can also act as analogues for earlier events such as that proposed for 2800 years BP in the early stages of the settlement of Western Polynesia  (Kirch 2010). The geological and archaeological findings indicative of palaeotsunamis within the wider Pacific region discussed above provide a fragmentary, but important record that is similar to the more comprehensive dataset developed in New Zealand  (McFadgen 2007).