dataesr/scientific-paragraphs-categorization huggingface dataset:
To explore the relationship between the Indian summer monsoon and the Indian Ocean WC, the Indian Institute of Tropical Meteorology homogeneous monthly all-India rainfall dataset available from 1871 to 2014 (e. g. ,  Parthasarathy et al. 1995)  is analyzed. Time series of all the climate indices are shown in Fig. 3 , with the linear trend for their common period of 1962-2009 being removed from each index.
Similarly, we remove ENSO's effect on Indian summer monsoon and Indian Ocean SST indices (e. g. ,  Klein et al. 1999; Du et al. 2009) , and the Atlantic SST effect on the monsoon index. These indices are shown in Figs. 3d-f. Then, we apply the Bayesian DLM to the residual Y 0 , with Y 0 5Y(t) 2 b 1 (t)ENSO(t) 2 b 2 (t)IOD(t), using the monsoon index as the predictor. Subsequently, we apply the DLM to Y 0 2 Y(monsoon), using Indian Ocean SST and Atlantic SST indices as predictors. We separately examine the monsoon effect versus Indian and Atlantic Ocean SST, to avoid overfitting with the limited data record for the SLM and DLM (e. g. ,  Babyak 2004 ). The objective of partial DLM is to sequentially remove the influence of the preceding predictors so that each predictor in the DLM is independent.
The seasonality of convection-WC covariability for both oceans is robust to cross-dataset differences using WASWind, NCEP-NCAR, JRA-55, and ORAS3 winds to represent the WCs, even though there are quantitative differences among datasets (figure  not   filtering. Averaged winds from all four-wind products for 1962-2005 are also tested, and we obtained similar results but with somewhat lower correlation with warmpool convection. Given that the covariability reduces considerably for convection with the Indian Ocean WC but only weakly with the Pacific WC during summer, the evident reduction over the Indian Ocean likely results from strong seasonality of the Indian Ocean WC. To confirm this point, we compare the winter and summer evolutions of the warm-pool convection, Indian Ocean WC, and Pacific WC, respectively (Figs.
8 ). The correlation coefficients between the WCs and zonal sea level gradient [WOA13 and  Ishii and Kimoto (2009)  average] are 0. 71 (. 90%) over the Indian Ocean and 0. 93 (. 95%) over the Pacific for the 1962-2009 period. For the Indian Ocean, the sea level anomaly (SLA) gradient is calculated by SLA averaged for 58S-58N, 808-958E subtracting that for 58S-58N, 658-808E, which are approximately the east and west portions of the Indian Ocean WC region (Figs. 5b  and 5d , respectively) and thus represent the WC effect on sea level gradient. For the Pacific, it is measured by SLA averaged for 58S-58N, 1308E-1808 subtracting that for 58S-58N, 1808-1308W, which are approximately the west and east portions of the Pacific WC (Fig. 5 ) defined by 2t x. Since the thermosteric sea level data are independent datasets from the reanalysis winds, their good agreements (see section 2a for scientific justification) increase our confidence in the decadal variations of the Indian-Pacific WCs detected by reanalysis winds since the 1960s.
3; Fig. 4 ), and the Indian and Pacific Ocean WCs are essentially uncorrelated (Fig. 6 ). Decadal variability of the Indian and Pacific Ocean WCs and the seasonality of their covariability are robust to cross-dataset differences. The WCs' decadal variations are also confirmed by the CCMP satellite winds and AVISO SSHA zonal gradients within the recent two decades (Figs. 5  and 7 ), and by the consistent variability of zonal gradients of the upper-700-m thermosteric sea level based on in situ observations before the satellite era (Figs. 5  and 8 ). The observed decadal variability of the Indo-Pacific WCs can be largely explained by decadal variability of ENSO, IOD, Indian summer monsoon convection, and basin-mean SST of the tropical Indian Ocean. Since this paper focuses on examining decadal variability rather than multidecadal trend (section 1), the linear trend for 1962-2009 is removed from each climate index (Fig.
Acknowledgments. Part of this work was completed when  Weiqing Han  was visiting NCAR during her sabbatical leave. She thanks  CCR/NCAR  for providing partial summer salary support. W. Han  is supported by  National Science Foundation (NSF )  AGS-1446480 ,  NASA OSTST NNX17AI63G ,  NASA OVWST NNX14AM68G , and  National Monsoon Mission Directorate  Award  SSC-03-002  from the  Government of India. G. A. Meehl  and  A. Hu  are partly supported by the  Regional and Global Climate Modeling Program (RGCM)  of the  U. S. Department of Energy's Office of Science (BER) ,  Cooperative Agreement   DE-FC02-97ER62402 , and the  National Science Foundation. Jessica Kenigson  is supported by  NASA   Harriett G. Jenkins Graduate Fellowship Program Grant   NNX13AR74H. The  National Center for Atmospheric Research  is sponsored by the  National Science Foundation.
Image analysis of surface roughness All images acquired by the three microscopes were analyzed with Mountains, a surface imaging and metrology software program (Digital Surf, Besancon, France), to calculate height-map roughness. Raw data measured by the three devices were imported into the software that accepted multiple format files. The use of the same methods of surface roughness calculation eliminated the bias linked to differences between the software programs of each instrument. Each height map was converted by the software into two roughness profile series, along the X and Y axes. Roughness was calculated to ISO 4287 (1997, Geometrical product specifications -Surface texture: profile method -Terms, definitions and surface texture parameters), as illustrated in Fig. 2. The roughness profile was defined as being derived from the primary profile by suppressing the long-wave component (high-pass) filter, with cut-off being λ c.
Second, we did not document occult HBV infection since HBV DNA was only tested in HBsAg-positive patients. This has probably underestimated the prevalence of HBV infection. Indeed, in one study conducted in Côte d'Ivoire, 10% of HBsAg-negative patients had detectable HBV DNA  [29]. Third, the lack of molecular data concerning the HDV as HDV RNA testing has become a more compelling tool for recognizing active replication. This may have overestimated the prevalence of HDV co-infection. Fourth, due to low amounts of plasma available, HBV DNA was not performed in all HBsAgpositive patients, and resistance and genotypic tests were not performed. In West Africa region, Genotype E is the predominant genotype  [30]. Finally, our study population was selected based on the local identification of HIV-2 and dually reactive patients.
Funding The WADA Collaboration is partly funded by the  National Cancer Institute (NCI) , the  Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD) , and the  National Institute of Allergy and Infectious Diseases (NIAID ) of the  US National Institutes of Health (NIH) , as part of the  International Epidemiologic Databases to Evaluate AIDS (IeDEA)  under Award #  U01AI069919. The  ANRS  ( France REcherche Nord &sudSida-hivHépatites ) supported part of the laboratory work performed within this study.
At a sharp edge with temperature-independent material properties, the factor is exactly f geo = 2. For non-linear material properties, the factor is f geo = 2. 1. The non-linearity is weak because the increase of heat capacity with temperature nearly compensates the decrease of heat conductivity, making the thermal effusivity nearly independent of temperature. The geometrical factor has been calculated by the finite element software package ANSYS ۛ for a range of edge angles and for a range of radius of curvature in the case of filleted (rounded) edges ( Fig. 5  ). To obtain this factor, heat flux was applied uniformly over an edge having an initial temperature T init = 100 °C. The peak temperature increase was divided by that obtained far enough from the edge that the heat flow into the bulk could be considered to be one-dimensional.
5 mM) and increasing doses of CaCl 2 (0. 1 to 5 nM) for 30 min, with or without addition of the calpain inhibitor MDL28170 (100 mM). Immunoblot analysis were performed using anti-GFP, -Capns1 andtubulin antibodies. The 18 kDa truncated Capns1 fragment is indicated by an arrow. DOI: https://doi. org/10. 7554/eLife. 27444. 008 decrease in RhoGDIa sumoylation could increase the recruitment of Rho GTPases at plasma membrane, thus facilitating their activation by Shigella for its internalization. As a first step, we analyzed the effect of depleting RhoGDIa on Shigella entry and actin polymerization in human epithelial cells. A significant increase in intracellular bacteria was visible 30 min postinfection in RhoGDIa knockdown cells when compared to control cells (Figure  6A -B and Figure  6 source data 1).
After washing, the sections were incubated with a goat anti-rabbit Cy3-conjugated secondary antibody (Jackson Immunotech) for 1 hr at room temperature. Nuclei were counternstained with DAPI, and slides were mounted (Prolong, Life technologies). All images were acquired using Apotome microscope (Zeiss). Pearson's correlation coefficient (Rr) was used as a measure of the co-localization and calculated using the colocalization studio plugin of Icy software  (Lagache et al. , 2015).
Acknowledgements We acknowledge  Chuanshu Huang  and  Mark R Philips  for the generous gifts of RhoGDIa plasmids. We thank  Peter A Greer  for providing the Capns1 WT and Capns1 KO MEFs. We are grateful to  Jacob S Seeler  for providing unpublished auxin-inducible degron-UBC9 HT1080 cells and for intellectual input. We also thank  Sandrine Etienne-Manneville  for helpful discussions. This work was supported by grants from  LNCC  ( Equipe labellisee ),  Odyssey-RE ,  INCa  and  ERC-AdG  ' SUMOSTRESS '. PL was supported by  LNCC. SF was supported by  EEC 'RUBICON' and Sidaction.
This included information provision on medicine and stem cells (Table  1 , Section 3), face-to-face discussion events with non-specialists, and researcher training and support on patient-and public-engagement (Table  1 , Section 5). In addition, in-depth articles were published on the EuroStemCell website, highlighting the clinical trials process, national and European regulatory processes, private stem cell clinics, stem cell tourism and for-profit clinical trials  [6]  -all optimised for search (see Section 5. 1. 3 for further detail). Providing access to current and credible information on stem cells, the applications of them in research and healthcare, and the social, moral and ethical implications of their use. Information is synthesised from many sources, written in clear language in summary and longer form.
The public engagement training provided by EuroStemCell is usually in the form of sessions scheduled into the programme of scientific events like annual meetings, conferences or summer schools. Multilingual functionality was identified as an essential development, and was added to the website from 2011 -translating the interface and key content into English, French, German, Italian, Spanish, and Polish and so making the site accessible to more than 80% of Europeans in their first or second language. Social media channels including Twitter, Facebook and YouTube were used to support all communication efforts, providing supplementary conversation and dissemination platforms, while raising the profile and extending the reach of the website, resources and direct public engagement. In an audience evaluation, in the form of an online survey disseminated through our partnership and networks carried out by a professional external evaluator in 2011, 95% of respondents (n = 240) felt the website provided reliable information and 86% said they would recommend it to their colleagues and friends.
These categories allow the project to meet the needs of a wide variety of audiences. They function to aid structuring of the information behind the scenes, while the 'visible' structure represented on the website is organised to retain flexibility and appeal to diverse audiences (see Table  1 ), using tagging and metadata to allow content to surface via appropriate filters. Dynamic provision of new and updated website content for each of these audience groups is key to the project's success, as is its availability in the six most commonly spoken languages in Europe (English, French, German, Italian, Spanish, and Polish)  [31] ). Topical, relevant, accurate content is more likely to rank highly in online searches and be found. Supporting this, EuroStemCell's platform and resources (including factsheets and digested reads) are optimized for search using best practices laid out by the World Wide Web Consortium (W3C), making it easier for search engines like Google to index the content.
This evaluation work was undertaken to inform the redevelopment of the website which was launched December 2016. Data are based on 240 respondents from 15 countries within the network. concludes that the goal of public engagement is not to evolve from dissemination of research via dialogue about research to public participation in research  [43]. Rather, they challenge the idea that these three models form a hierarchy, and conclude that there is a place for all three in public engagement with science  [43]. As a project, we co-ordinate the flow and exchange of information in a timely and accessible manner, with the primary aim of stimulating engagement and two-way communication between the scientific community and other communities about stem cell research. A useful means of conceptualizing this approach to information provision is as follows: at one level, EuroStemCell views its role as providing 'information for dialogue'; however, because an ethos of co-production underpins all of the information-provider work of the project, this can be extended to 'information as dialogue'.
Acknowledgements EuroStemCell receives funding from the  European Union 's  Horizon 2020 research and innovation programme  under grant agreement No  652796. It has previously been funded under the European Union's Framework 6 and Framework 7 funding streams under grant agreements  503005  and 241878 respectively. The project has also been supported by a number of EC-funded research consortia,  ESTools, OptiStem, EuroSyStem, NeuroStemCell, ThymiStem, HumEN, PluriMes ,  Neurostemcell Repair , and  Repair HD  under grant agreement Nos 018739 (ESTools), 223098 (OptiStem), 200720 (EuroSyStem), 222943 (NeuroStemCell),  602587  (ThymiStem),  602587  (HumEn), 602423 (PluriMes),  602278  ( Neurostemcell Repair ), 602245 (Repair-HD). The authors would like to thank  Anna Couturier ,  Dr Deirdre Davison ,  Sarah Jenkins ,  Professor Austin Smith ,  Amanda Waite  and the reviewers as well as editors for helpful comments on the manuscript.
Identification of SCD1 as a Downstream Target of miR-600 To identify the mechanism(s) whereby miR-600 exerts its biological effect on bCSC, we established the gene expression profiles of fluorescence-activated cell sorting (FACS)-sorted SUM159 ALDH br cells transiently transfected with either miR-600 OE vector or its corresponding control vector (Figure  3A ). We observed an overrepresentation of miR-600 predicted target genes (ArrayExpress: E-MTAB-5393 and TargetScan database;  Garcia et al. , 2011)  among the genes downregulated after miR-600 OE (p value < 0. 01; false discovery rate [FDR] < 0. 25) (Figure  3B ; Table  S2 ). Because target gene prediction of miRNAs is challenging due to mismatch tolerance in miRNA-target mRNA complementarity, we used MiRonTop algorithm to integrate our gene expression profiles with miRNA target prediction datasets into a single meta-analysis  (Le Brigand et al.
, 2010). This algorithm selects significantly downregulated transcripts following the overexpression of a specific miRNA and generates enrichment scores according to the spatial distribution of predicted miRNA target sites along the selected transcripts. MiRonTop analysis validated the enrichment of miR-600 predicted targets in the population of downregulated transcripts (Figure  3C ). We focused our next set of experiments on a subset of 19 transcripts with the highest enrichment score (log2 fold change <À0. 7; p value < 0. 01) (Table  S3 ). To functionally validate these  (B) Volcano plot of the gene expression profiling results. Scatter points represent genes, the x axis is the log2 fold change of the gene expression ratio between ALDH br miR-600 OE treated versus untreated cells, and the y axis is the probability that a gene has statistical significance in its differential expression (genes with a FDR > 0.
25 are highlighted as black dots). miR-600 predicted target genes from TargetScan database are highlighted as red dots. (C) Graph derived from MiRonTop bioinformatics tool showing the overrepresentation of miR-600 seed complementary sequences in the 3 0 UTR of downregulated transcripts. Representation of TargetScan predicted targets in the set of downregulated genes was compared with the set of all expressed genes. For (legend continued on next page) 19 transcripts as miR-600 targets, we performed a STarS (suppressor target screen) assay  (Polesskaya et al. , 2013) , an unbiased screening approach to identify miR-600 functional targets. The STarS assay relies on the screening of a focused small interfering RNA (siRNA) library targeting the 19 MiRonTop selected transcripts, each siRNA being systematically and individually co-transfected with miR-600 LNA.
Gene Expression Profiling RNA expression data were generated using Affymetrix ST2. 0 oligonucleotide microarrays as described in Supplemental Experimental Procedures. SCD1 3 0 UTR Reporter Assay To validate miR-600's direct interaction with SCD1, we developed a reporter assay using two plasmids (LightSwitch Luciferase vector) with luciferase expression under control of either the wild-type SCD1 3 0 UTR (SCD1-WT) or the SCD1 3 0 UTR with mutations brought into the seed sequence of miR600 site (SCD1 mutant). We also used a Cypridina TK Control Vector (Active Motif) as reporter of transfection efficiency. 24 hr post-transfection, luciferase expression was revealed using LightSwitch Dual assay kit (Active Motif) according to the manufacturer's instructions. Data were first normalized to the Cypridina TK control vector and then expressed as the SCD1-WT/SCD1 mutant ratio.
Statistical Analysis GraphPad Prism 5. 0 was used for data analysis and imaging. Results are presented as the mean ± SD for at least three repeated independent experiments. To investigate associations among variables, univariate analysis were performed using non-parametric Wilcoxon rank sum test, chi-square test or Fisher's exact test when appropriate. Extreme LDA (http://bioinf. wehi. edu. au/software/elda/) was used to evaluate bCSC frequency. GSEA significance cutoffs were FDR < 0. 25, p < 0. 05. The Kaplan-Meier method was used to establish survival curves, and curves were compared with the log-rank test. In all cases, a p value < 0. 05 was considered as statistically significant.
ACKNOWLEDGMENTS We express our gratitude to the  Fondation ARC  for supporting the acquisition of our cell sorter. Thanks are due to the  MetaToul-Lipidomique Core Facility  ( I2MC ,  INSERM 1048 , Toulouse, France),  MetaboHUB - ANR-11-INBS-0010 , the  CRCM  flow cytometry and animal core facilities. We thank  Gisele Froment ,  Didier Ne  `gre, and  Caroline Costa  from the lentivectors production facility/ SFR BioSciences Gerland-Lyon Sud  ( UMS3444/US8 ). This study was supported by.
The transmitted intensity spectrum (I T and I 0 ) is recorded with a spectrograph/camera system (described below) that is adjusted to provide a modest spectral resolution of 0. 3 nm, which is still sufficient to resolve the product of light source and intrinsic transmission line shapes. Since the line shape of the light source does not fully cover the absorption cross section, spectrally resolved data (measurement and cross section) is required for determining the ozone density according to equations 1 and 2. The two-beam UV-LED absorption setup is in Mach-Zehnder configuration as shown in figure  3. The used UV-LED light source (UVTOP, 255-TO18-FW) provides a spectrum with a centre wavelength of λ = 255 nm and FWHM of ∆λ = 11 nm, see figure  2. It is attached to a mounting head that is actively temperature-controlled through a piezo element, and driven by a stabilised current/power supply unit (Thorlabs, LTC100).
9 × 10 13 cm -3 from the ratio calculation. Due to the significantly reduced uncertainty, the reference beam correction was used throughout this article for O 3 density measurements. A single measurement for each of the four quantities (I P L , I P , I L , and I BG ), their reference values and the respective ozone density value according to equation 2 is obtained from one full triggering cycle of 10 s (see figure  8 ). 50 consecutive measurements for each quantity were recorded and statistically averaged to derive the ozone density data presented. With the plasma source attached to a three-axis manipulation stage, spatially resolved O 3 densities were measured along the 30-mm long plasma channel as shown in figure  10. The O 3 density is found to increase from the gas inlet at -30 mm towards the centre at -15 mm.
g. [53]  and references within, since the high collisionality under atmospheric pressure ensures a full rotationaltranslation equilibrium. The applied numerical spectra simulation and fitting procedure has successfully been cross-checked against other commonly used software, e. g. LIFBASE, and applied before  [28, 63]. In order to conduct the gas temperature measurements, a very small air gas leak in the feed gas tube of the plasma source had to be introduced as an impurity. Its influence was checked to not change the ozone density within the corresponding measurement accuracy. The detection system was operated with a FWHM of 0. 29 nm at λ = 380 nm, and with a total camera exposure time of 30 s. The results of the rotational/gas temperature measurements under our experimental conditions exhibit an absolute uncertainty of about ±10 K as a typical deviation between the evaluation of different rotational bands of the second positive system of molecular nitrogen (not shown), but a smaller relative/statistical uncertainty of ±5 K for repeating the measurement or parameter variation.
Global model In order to better understand the production and destruction of reactive species in cold atmospheric pressure plasmas zero-dimensional global models are often employed  [64]. Here, the zero-dimensional plasma-chemical kinetics model GlobalKin  [55, 56]  is used to identify and analyse the production and destruction mechanisms of reactive species within the investigated atmospheric pressure plasma. GlobalKin consists of three modules; a reaction chemistry and transport module, a two-term Boltzmann equation solver for the electron energy distribution function (EEDF), and an ordinary differential equation (ODE) solver. GlobalKin calculates absolute species densities accounting for different production.
The fact that O 2 (b 1 Σ + u ) is increasing more strongly with power than O at a constant gas temperature explains the decrease of O 3 in fig. 17 + u ) + O 3 ). All data shown is taken from the simulations using the upper limit of the gas flow velocity. calculated gas temperatures obtained from the GlobalKin simulations. While the O and O 2 (b 1 Σ + u ) densities show approximately the same trends as previously discussed for the fixed-temperature case, the normalised rate coefficients now also show a clear dependence on power, because the calculated gas temperatures increase with power, as shown in fig. 16. In particular, the rate coefficient for production of O 3 decreases A c c e p t e d M a n u s c r i p t strongly, while the rate coefficient for consumption increases weakly. Both trends lead to a further decrease of O 3 densities with power.