dataesr/scientific-paragraphs-categorization huggingface dataset:
Mean capture efficiencies, prior distributions, posterior distribution and point estimate datasets used in this study Mean capture efficiency was set at 0. 03 throughout the manuscript except for Supplementary Fig. 2c  and 3c where a capture efficiency of 0. 06 calculated from smFISH data was used. Prior distributions where generated as follows: Fig. 1c, 4 , and Supplementary Fig. 2b, 3c, 4c, , 6b-c data were normalised using "global" priors obtained from all cells in the dataset in order to correct for batch effects. Supplementary Fig. 2c  used priors calculated from rapidly growing cells. Fig. 2a, 2de , Supplementary Fig. 3a-c  data were normalised using "local" priors estimated within each individual dataset to exclude any residual contribution of batch differences to HVG calls. Figure  3c  and Supplementary Fig.
2a ). Identifying HVGs from scRNA-seq experiments is challenging due to the strong technical noise present in the data and several teams have addressed this problem  64, [66] [67] [68]. The general consensus is to decompose the total noise observed into its technical and biological components. To do this, the dependence of technical noise to the mean is measured and used to infer potential additional biological noise present for each gene (Fig. 2a , Supplementary Fig. 3a ). Here, we have developed an original method for HVG detection based on bayNorm normalised data and sets of computed synthetic control RNA-seq data (synRNA) to estimate noise floors. synRNA are generated as follows: Given a scRNA-seq dataset with a raw count matrix   and a vector of estimated cell-specific capture efficiencies   , we produced a set of synRNA data 𝑥𝑥 𝑖𝑖𝑖𝑖 syn = Binom(𝑥𝑥 𝑖𝑖𝑖𝑖 Poisson , 𝛽𝛽 𝑖𝑖 ) Finally,   syn data are normalised with bayNorm using prior parameters estimated from the original raw data (i.
e. identical to those used for normalisation of the cells data). To identify highly variable genes, a local regression between noise and mean expression of all genes from the normalized synRNA dataset is calculated and compared to the noise levels observed in the corresponding normalised experimental datasets (log-log, Fig. 2a ). To call genes with noise levels significantly above the synRNA fitted line, we use an approach similar to the one proposed in ref  64  and based on an adaptation of the gene expression variation model  68. Briefly, vertical differences (only considering positive residuals) between noise levels in the experimental dataset and the fitted line were calculated (illustrated as ΔCV on Fig. 2a ). The differences were normalised by dividing by the residuals from the regression, which follow a normal distribution.
Most genes were assumed not to deviate from the centre of the distribution significantly. The centre was found by the kernel density of the normalized differences. Next, a normal distribution was fitted using differences which were below that centre. P-values were then extracted based on the normal distribution and adjusted using the Benjamini and Hochberg procedure. Noisy genes were called independently for each batch of 96 cells or ctrRNAs generated in this study after normalisation with bayNorm using priors estimated within each dataset ("local" priors). For each gene in each dataset, noise and mean values across cells where calculated using pooled expression scores of 100 samples of the bayNorm posterior distribution per cell. Using this design, gene variability was assessed in 100 bootstrapped versions of each dataset.
Genes were called noisy if they had an FDR < 0. 1 in 85 or more bootstrap samples. Genes called in at least one rapid growth cell dataset (2502_1, 2502_3, 2502_5, 2502_7, 2502_9, 1904_1, 0109_3, 1711_1, 1711_2), and none of the ctrRNA datasets (2502_2, 2502_4, 2502_6, 2502_8, 2502_1, 1904_2, 0408_5), were called HVGs and are discussed further in this study (Supplementary Table  6 ). Functional analysis of HVG (Fig. S4d ) Levels of quantitative variables describing a series of genes features were compared between HVGs (including or not the top-500 periodic genes) and all other genes from the high confidence set using one-sided Wilcoxon tests. Features were obtained from four studies and are listed below  19, 34, 35, 37. Labels were adjusted to be self-explanatory and a detailed description of each feature is available in the original publications.
05). Differential Gene Expression analysis (Fig. 3c , Supplementary Fig. 5d-e ) Several Differential Expression (DE) analysis methods, tailored for scRNA-seq analysis have been published. A recent comparative analysis  69  and our own experience identifies MAST  70  as a reliable method. Therefore, in this study, we used the MAST package with method = "glm", the "ebayes" option enabled, and considering adjusted P-values from the continuous part of the hurdle model utilized in MAST (multiple testing adjustment method: Benjamini and Hochberg)  70. DE detection was run independently on 100 bayNorm posterior distribution samples for Fig. 3. Genes called DE in > 90% of the posterior distributions were considered differentially expressed. Log2 ratios are the mean of the Log2 ratios from each posterior distribution.
Representative smFISH images are shown for low-variability control rpb1 mRNA and three mRNAs with different levels of variability (lsd90, mot1, and SPAC27D7. 09c, see also Supplementary Fig. 2c, 3c-d). Scale bars representing 5μm and sizecorrected Fano factors (scFano) are indicated on each plot. (c) Boxplot showing size-corrected Fano factors measured by smFISH for HVGs (n=8 genes) or control genes (n=5 genes). P values for a onesided Wilcoxon test are shown above the figure. Boxplots represent median, interquartile range, and most extreme data points that are not more than 1. 5 times the interquartile range. (d) Functional analysis of variable genes from 9 datasets of 96 cells (n=864 cells) during rapid proliferation. Significance of overlap of variable mRNAs in each dataset with selected functional categories is shown (-log10 of PFisher one-sided for overlap of HVGs from each dataset and each category, p-values are corrected for multiple testing using Benjamini and Hochberg, number of tests = 14 categories/dataset, as shown on the figure).
syn with similar mean expressions and capture efficiencies as the real experimental data but with no biological variability above what is expected from the Poisson distribution. Poisson noise is the minimal amount of noise expected if no additional biological variability is present. To do this, we first generate a gene expression dataset   Poisson sampled from a Poisson distribution with mean expression obtained from raw count matrix   and capture efficiencies   : Both means above are calculated across cells (index ). In a final step, we used binomial downsampling to generate a   syn dataset from   Poisson simulating the effect of partial RNA capture during the scRNA-.
Acknowledgements We thank  Tom Livermore  for his help during the initial part of this project and  Claire Stefanelli  for her contribution to bayNorm development. We are grateful to  Simona Parrinello ,  Amalia Martínez Segura  and  Miles Priestman  for their input on the manuscript. This research was supported by the  UK Medical Research Council , a  Leverhulme Research Project Grant  ( RPG-2014-408 ), and a  Wellcome Trust   Senior Investigator Award  to  J. B. (grant  095598/Z/11/Z ). It used the computing resources of the  UK Medical Bioinformatics partnership (UK MED-BIO) , which is supported by the  UK Medical Research Council  (grant  MR/L01632X/1 ) and the  Imperial College High Performance Computing Service. All figures except 1a and S2a contain original data.
syn with similar mean expressions and capture efficiencies as the real experimental data but with no biological variability above what is expected from the Poisson distribution. Poisson noise is the minimal amount of noise expected if no additional biological variability is present. To do this, we first generate a gene expression dataset   Poisson sampled from a Poisson distribution with mean expression obtained from raw count matrix   and capture efficiencies   : Both means above are calculated across cells (index ). In a final step, we used binomial downsampling to generate a   syn dataset from   Poisson simulating the effect of partial RNA capture during the scRNA- seq procedure: 𝑥𝑥 𝑖𝑖𝑖𝑖 Poisson = Poisson(𝜆𝜆 𝑖𝑖 ), where 𝜆𝜆 𝑖𝑖 =< 𝑥𝑥 𝑖𝑖𝑖𝑖 ∑ 𝑥𝑥 𝑖𝑖𝑖𝑖 𝑖𝑖 𝑖𝑖 >< (� 𝑥𝑥 𝑖𝑖𝑖𝑖 )/𝛽𝛽 𝑖𝑖 >.
All children received advice from a dietician for the implementation of a cholesterol-lowering diet during the six months before statin therapy. According to local expert opinion, a statin was prescribed when the LDL-C level remained > 160 mg/dl in the presence of another cardiovascular risk factor (obesity, diabetes, high blood pressure, lipoprotein (a) > 500 mg/l) or > 190 mg/dl in the absence of a cardiovascular risk factor. Children with homozygous familial hypercholesterolemia were excluded. The following clinical and epidemiological data were collected for each patient: age, sex, weight, height, family history of first-or second-degree hypercholesterolemia, with or without cholesterollowering treatment, and history of early cardiovascular events in a first or second degree relative. The Waterlow score, consisting of the weight divided by the expected weight for the child's height (as a percentage), and the height divided by the expected height for the child's age (as a percentage) were used to evaluate growth  [14].
Puberty was assessed by Tanner stage. Patients were generally seen once or twice a year at follow-up. Before each consultation, a fasting lipid test was performed, including plasma TC, HDL-C, and TG levels (by enzymatic colorimetric method) and LDL-C level (calculated using the Friedewald equation). The liver enzymes aspartate aminotransferase (AST) and alanine aminotransferase (ALT) and the muscle enzyme creatinine phosphokinase (CPK) were assessed at the same time. The efficacy of treatment was evaluated first, by the decrease (as a percentage) in TC and LCL-C levels following statin therapy between the start of treatment and the last follow-up consultation and second, by the percentage of children who achieved an LDL-C level < 160 mg/dl. At each consultation, data on self-reported undesirable clinical effects potentially related to the treatment were collected: cramps, unexplained muscle pain, weakness or stiffness, asthenia, abdominal pain, and headache.
Biological tolerability was assessed by searching for muscle-related adverse effects, defined as a rise in CPK levels to more than five times above normal (5N). An elevation of ALT and/or AST levels to more than three times above the laboratory-defined upper limit was considered to be a sign of hepatic cytolysis. The global tolerability of treatment was assessed by monitoring the occurrence of clinical or biological side effects, their severity, the need to change the statin, the regularity of increase in height and weight, and pubertal development. When none of these side effects occurred, we considered that statin therapy was well tolerated. The study was approved by the local ethics committee. Statistical analyses were performed using GraphPad Prism software (version 7. 03). The Wilcoxon test, with sample matching, was used to compare clinical and laboratory measures between the start of statin therapy and the end of follow-up.
, 2014; Willems et al. , 2017). The French Guiana Exclusive Economic Zone (EEZ, 4-9°N, 49-54°W) covers 132,000 km² and extends 200 nautical miles (nm) into the Atlantic Ocean, including a broad continental shelf, a slope and an abyssal plain. The slope seems to be an important habitat for cetaceans based on previously documented high encounter rates and species richness  (Miloslavich et al. , 2011; Mannocci et al. , 2013). In autumn 2017, an environmental baseline survey was conducted in the slope to collect data before an oil and gas drilling project. This survey provided some valuable mammal and seabird sightings which improve knowledge about marine biodiversity of the area. This study aims to describe the species diversity of cetaceans and seabird, opportunistically sighted during this scientific survey off French Guiana, and to discuss the ecological importance of the area.
MATERIALS AND METHODS During October and November 2017, a scientific survey was conducted off French Guiana, mainly on the slope, to study the offshore ecosystems focusing on the quality of sediments and water as well as the benthic and planktonic communities concerning oil and gas development. The integration of biodiversity knowledge within oil and gas exploration activities is part of the approach concerning the protection of biodiversity  (Chaineau et al. , 2010). Three marine fauna observers (MFOs) recorded opportunistic sightings data on marine mammals and seabirds during this survey.
Family Comnon long vessels served as a platform for opportunistic marine megafauna observations. The visual monitoring protocols were based on international standards (JNCC) and conducted by three experienced MFOs. Two MFOs visually scanned the water simultaneously when the vessel was underway; they scanned a 180° arc ahead of the vessel. When the vessel was stationary or maneuvering for benthic sampling, only one MFO actively scanned the water and other MFOs were in a break or entering data in the database. Shifts were organized so that each MFO observed for two hours and then had a one-hour break. Observations were conducted with the naked eye from the upper deck of the vessel or the bridge. Binoculars (7×50) and a reflex camera with a 70-300 mm lens were used to identify species. Identification was made to the lowest taxonomic level possible.
The distance to the sighted cetaceans, turtles and landed seabirds was determined using the binocular's reticles or rangefinder sticks. The distance to flying seabirds was estimated with naked eyes by experienced MFOs. The bearing of the animals was determined using an angle-board. Data collected also included environmental informations such as weather, sighting conditions, vessel activity, course, speed and position. Sighting informations included species identification, time (GMT), number of indivi-duals, behavior (swimming speed, flying behavior, diving, breaching, milling, bow riding and foraging behavior) and presence of calves/juveniles. Sightings of marine mammals, seabirds, sea turtles, large pelagic fishes and anthropogenic activities were recorded. All the maps were made using QGIS 2.
ACKNOWLEDGMENTS We thank  Romain Le Gall ,  Thibault Schvartz ,  Sébastien Thorin  and  Ken Deslarzes  for their help and support during all phases of this work. The Créocéan and R/V Proteus teams for their help during the survey;  Claire Pusineri  for her help with the overview on existing knowledge regarding marine mammals off French Guiana;  Amy Whitt  for her careful review and impro-vement of this manuscript. We also thank  Mauricio Cantor  and one anonymous reviewer for their comments and suggestions to improve the quality of this manuscript. The survey was funded by  Total E&P Guyane Française  and managed by Créocéan.
QUANTIFICATION AND STATISTICAL ANALYSIS All data were obtained using cells from at least three independent culture preparations or at least three independent animals per genotype. Repeats for experiments and statistical tests carried out are given in the figure legends as N numbers and refer to number of cells unless otherwise stated. Statistical analysis was performed using the Graphpad Prism v7. 00 software (GraphPad Software, Inc. , La Jolla, CA, USA). Mann-Whitney tests were performed for between-group comparisons. Survival differences were determined using the Kaplan-Meier method and the Log-rank test. All tests were two-tailed. (not significant [ns], p > 0. 05; * p < 0. 05; ** p < 0. 01; *** p < 0. 001).
ACKNOWLEDGMENTS The authors thank the confocal microscopy image facility. This work was supported by grants from  ANR   JC  ( ANR-17-CE17-0002-01 ),  DIM1HEALTH  ''action financee par la  Region Ile-de-France ,'' and  LabEx Inflamex  ( ANR-11-IDEX-0005-02 ). R. C. M. was supported by the  Equipe Program of the Fondation pour la recherche medicale (FRM). C. d. T. was supported by  FRM  ( 41482 ). The authors thank  Dr. Cedric Vonarburg  and  CSL Behring  for providing human monomeric pdIgA. We are indebted to the patients and healthy volunteers who participated in the study.
The irradiation was triggered when the nucleus reached a central position in the AB cell. Time series of micro-irradiated embryos were created using Image J software (http://rsbweb. nih. gov/ij/). A minimum of five embryos were analysed for each experimental group. Immunofluorescence staining. Freshly extracted embryo populations were immediately fixed in cold 4% (w/v) paraformaldehyde and their eggshells were freeze-cracked by placing at -20 °C during 15 min. Then, embryos were pelleted via centrifugation (2 min. , 2000 rpms, RT) and paraformaldehyde replaced by cold acetone for permeabilization (2 min, -20 °C) and, finally twice washed in M9. After fixation and washing, M9 was removed and replaced by a freshly prepared solution of phalloidin-AF 594 (10:1000 (v/v), Molecular Probes) and Hoecsht 33342 (2:5000 (v/v), Molecular Probes).
Embryos were incubated overnight at RT under gentle agitation and then washed via two series of centrifugation (2 min. 2000 rpms) with M9. The supernatant was discarded and the pelleted embryos suspended in 2-3 drops of Prolong Gold Antifade reagent (Molecular Probes) and transferred by pipetting for mounting between glass slides using ProLong ™ Antifade Gold Reagent (Invitrogen). Three-dimensional images were acquired with a Leica DMRE TCS SP2 AOBS confocal microscope (oil-immersion objective × 63, 1. 4 NA), assembled, and reconstructed using Image J software. Monte Carlo simulation. Geant4-DNA  [41] [42] [43] [44]  , the open source very low energy extension of the Geant4 Monte Carlo simulation toolkit  [45] [46] [47]  , was used for this work (release Geant4. 10. 3. p01). We used a physics list based on the recommended "G4EmDNAPhysics_option4" constructor  44.
The methodology for converting confocal image data into a 3D phantom has been described previously in Barberet et al. 22. The set of images of the 2-cell stage embryos acquired from the confocal microscope was transferred into the public domain ImageJ software (http://rsbweb. nih. gov/ij/) for 3D reconstruction (Fig. 1a, b ). An intensity threshold was then applied for each colour channel to separate fluorescent objects from the background in each slice of the stack. The nuclear volume was defined as the green channel by manually selecting a ROI around the chromatin on the red channel based on contrast selection, and cropping the region outside the ROI (Fig. 1c ). The chromatin, nuclear volume and embryo volume could be extracted into an individual text file containing: (i) the total number of voxels for the 3 channels (Red, Green and Blue), (ii) the voxel size along the 3 dimensions, (iii) a position shift in order to centre the embryo in the simulated irradiation dish, (iv) the list of each voxel's position and material composition, as well as the intensity fluorescence content of the voxel.
Acknowledgements The AIFIRA facility is financially supported by the  CNRS, the university of Bordeaux  and the  Région Nouvelle Aquitaine. We thank the technical staff members of the  AIFIRA  facility  P. Alfaurt  and  S. Sorieul. MS was supported by the  Region Aquitaine (POPRA). This work has been partly supported by the  European Community  as an  Integrating Activity "Support of Public and Industrial Research Using Ion Beam Technology" (SPIRIT)  under the EC contract no. 227012. GM was supported by the  European Community  as an " Integrating Activity Supporting Postgraduate Research  with  Internships in Industry and Training Excellence" (SPRITE)  under  EC  contract no. 317169. The project was supported by the  French national Centre for Scientific Research (CNRS, Mission Interdisciplinaire NEEDS).
Summary and conclusions In this study, the occurrence of FLCs in the Namib Desert, derived from 14 years of satellite observations, is systematically analyzed within the context of the regional climate and related to large-scale patterns of MSLP, Z500, T2m, LTS, SST, and TCWV, as well as Q and winds at different pressure levels from ERA5 reanalyses. The satellite data set of FLC occurrence is separated into FLC days and clear days, which are further investigated in terms of their meteorological conditions, air-mass histories, and statistical predictability during two seasons (AMJ and SON). It is found that MSLP and Z500 patterns on FLC days are systematically and significantly different from clear days on synoptic scales. On FLC days, a systematic pattern of significantly lower MSLP over continental southern Africa is observed, which, in combination with higher pressure over a marine coastal region at about 20 • S, leads to an onshore flow anomaly of marine boundary-layer air.
Acknowledgements. Funding for this study was provided by  Deutsche Forschungsgemeinschaft (DFG)  in the project  Namib Fog Life Cycle Analysis (NaFoLiCA) ,  CE 163/7-1. HA acknowledges receiving a  Research Travel Grant  from the  Karlsruhe House of Young Scientists  that supported a stay at  ETH Zürich  and thus facilitated the collaboration with Sebastian Sippel. The contribution of  Julian Quinting  was funded by the  Helmholtz Association  (grant  VH-NG-1243 ). Marco Gaetani  was supported by the  French National Research Agency  under grant agreement no. ANR-15-CE01-0014-01  ( AEROCLO-sA ). We acknowledge support by the  KIT-Publication Fund of the Karlsruhe Institute of Technology. We thank the three anonymous reviewers for their valuable and constructive comments. Financial support.
Statistics Genetic data were analysed using SPSS and Plink software v. 1. 07 [19]  to generate linear regression models, assessing the effect of rs35568725 on C-IMT phenotypes. Covariates included age, sex, plasma lipid levels and multi-dimensional scaling (MDS) dimensions 1-3 to adjust for population substructures over the pan-European population. Experimental data were plotted and analysed using nonparametric tests in GraphPad Prism 7; all data are either presented as mean AE standard error (SEM) or median and inter-quartile range (IQR) as indicated. P-values <0. 05 were considered significant and multiple-testing adjustments were applied where appropriate.
001, Fig. 3(b ). Observed effects on cholesterol efflux were partly dependent on intact autophagy since deregulation of autophagy by bafilomycin A1 supplementation ablates the beneficial effects of the Pro251 variant on cholesterol efflux to apoA1, Fig. 3(b). Ablation of the beneficial effects of Pro251 was accomplished by supplementing this system with 2. 5 lmol L À1 27-HC, further the effect of autophagy was diminished, Fig. 3(c). In line with data herein, autophagy flux was augmented by ~2-fold in oxLDL-treated human primary monocyte-derived macrophages carrying Pro251 compared to noncarrying cells, as measured by LC3 lipidation and p62 accumulation upon bafilomycin A1 supplementation (P = 0. 038 and P = 0. 016, respectively), Fig. 3(d-f ), see also Fig. S2A. Additionally, the immunophenotype of monocytederived macrophages was assessed using a coexpression approach as well as 10-plex electrochemiluminescense assay for cytokine production.