dataesr/scientific-paragraphs-categorization huggingface dataset:
The cytoplasmic sap was ultracentrifuged over a 60% w/v sucrose cushion. The resulting opalescent pellet was resuspended and further analysed by isokinetic centrifugation. Under these conditions, the ribosomal L7 protein and FMRP were detected at the level of polyribosomes (Fig 1B ), as previously documented  [20, 21] , indicating that polyribosomes could be separated from the 60-70% sucrose interface. Also, both proteins were present at the 60-70% w/v interface, but penetrated the sucrose cushion as they also appeared in lower fractions. To confirm that the material present at the interface did correspond to granules, samples were examined by electron microscopy following negative staining. Electron dense round shaped particles ranging from 100 to 800 nm were observed (note the extended scale in Altogether, these data demonstrate that a fraction enriched in granules is obtained at the interface under the conditions described here.
Proteomic analyses of granules preparations To reveal the protein content of polyribosomes and granules purified by isopynic centrifugation in Metrizamide gradients, fractions were analysed by Mass Spectrometry (MS). A total of 128 proteins sharing at least 1 peptide with known proteins registered in databases were found in granules (Fig  5  and S1 Table) , while 155 proteins were present in polyribosomes. Gene ontology-based pathway enrichment analyses revealed that the most significantly enriched biological processes in granules were notably 'translational elongation' (adjusted p-val = 2,67. 10 -12  ), 'RNA processing' (adjusted p-val = 1,38. 10 -1  ), 'ribonucleoprotein complex biogenesis' (adjusted p-val = 1,41. 10 -1  ) and 'cytoskeleton-dependent intracellular transport' (adjusted p-val = 3,40.
However, since Antar et al. [36]  have reported that only approximately 50% of FMRP colocalizes with ribosomal RNA and as we observed that not all granules contain FMRP (Fig 3G ), we decided to determine to which extent FMRP colocalizes with the ribosomal marker L7 in dendrites. We performed immunofluorescence analyses on rat hippocampal neurons in primary cultures using IgY#C10 anti-FMRP and anti-L7 antibodies. Deconvolution and binary merging analyses of images using the MetaMorph Software enabled us to study L7 and FMRP colocalization in 4534 granules spread over 15 dendritic segments (Fig  10A ). Several observations could be made from these colocalization studies. Firstly, the population of puncta positive for L7 is 2. 5 fold larger than the FMRP one. Secondly, L7 and FMRP co-localize in 30% of the puncta.
Immunofluorescence and live imaging Hippocampal neurons grown on coverslips for 10-12DIV were processed for immunofluorescence. Rabbit anti-FXR1P #ML13, chicken anti-FMRP #C10, mouse anti-FXR2 and rabbit polyclonal anti-L7 primary antibodies were used at 10 times less than the dilutions used for immunoblot analyses (see above), followed by Alexa secondary antibodies (green, red, blue respectively). Samples were mounted in Prolong Gold medium (Invitrogen). Images were captured using a Zeiss LSM 510 confocal microscope and a 63x (1. 4 NA) objective and analysed using the MetaMorph Software. For time-lapse videomicroscopy experiments, hippocampal cultures were transfected using Lipofectamine as described  [86]  with the pShuttle/GFP-FMR1 under the synapsin promotor, ensuring a neurospecific expression of FMRP.
The vector was engineered by subcloning GFP-FMR1 cDNA from pGFP-C2/FMRP construct  [38]  into the pShuttle (Stratagene) downstream of the synapsin promotor. Cells were imaged at 36°C-37°C in an open perfusion (0. 2-0. 5 ml/ min) Qe-1 RC-41LP chamber (Warner Instruments) mounted onto a Zeiss Axiovert inverted microscope equipped with a 63x (1. 4 NA) or 100x (1. 3 NA) objectives. Images were captured with a cooled CCD camera (Cool Snap HQ, Roper Scientific) every 5 sec for 20 min. The intensities of fluorescence along the processes of each neuron were measured with a user-defined threshold with the MetaMorph software (Universal Imaging). The mean movements of granules were measured on a 20 minutes scale using the SpotTracker plugging of the ImageJ software (NIH, Bethesda).
Scaffold software was used to validate MS/MS based peptide and protein identifications  [92]. Peptide Prophet algorithm was used for peptide identification with a 95,0% confidence  [93]. Protein identifications were accepted on the basis of at least 1 identified peptides. Protein probabilities were assigned by the Protein Prophet algorithm  [94]. Proteins that contained similar peptides and could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony. To provide a semi-quantitative appreciation of protein abundance, the dedicated function of Scaffold software was used to normalize individual protein spectral counts data to the total spectral counts for each MS samples. The data presented in S1.
A simple direct comparison between treatments was done in full dye swap. Microarrays slides were then washed and scanned with the PowerScanner (Tecan, Männedorf, Switzerland) and analysed with the Array-Pro Analyzer software (MediaCybernetics, Bethesda, MD, USA). Microarray data were pre-processed and analysed using the FlexArray 1. 6. 1 (http:// genomequebec. mcgill. ca/FlexArray). Raw data correction consisted of a Lowess intra-array normalization and Quantile inter-array normalization. Statistically significant variations were detected using Limma (Bioconductor). Multiple hypotheses testing correction was done using the Benjamini-Hochberg procedure  [95]. Differences in gene expression were evaluated by calculating the fold of change (FC) of signal intensity in granules preparations versus polyribosomal preparations.
Acknowledgments We thank  Richard Janvier  and  Alain Goulet  from the  Electron Microscopy Core Facilities  for their precious help,  Ann Lorrain  for her generous gift of the pShuttle-synapsin-GFP plasmid,  Francine Nault  for neuron cultures,  Mélanie Allard  for 3D reconstitution,  Jérôme Lang  for technical assistance and  Gilles Charpenet  for critical reading of the manuscript and corrections.
This work was supported by grants from the  Canadian Institutes of Health Research (CIHR)  and the  Natural Sciences and Engineering Research Council of Canada (NSERC)  to EWK and PDK. LD was supported by the  Marie Curie European Community Programs  ( FP6 MEIF-CT-2006-41096  and  FP7-PEOPLE-ERG-2008-239290 ), CR by the  Fonds Québécois de la Recherche sur la Nature  et in for FMRP in granules biology. avenues for the study of RNA granule dysfunctions in animal models of nervous system disorders, such as Fragile X syndrome.
Initial feedback was generated automatically from the MAP system using monitoring information entered by the participant and data from the provincial administrative database sent to MAP from the Medical Office for the twenty first century (MOXXI), an electronic health record with a prescription and computerized drug and disease management system. A summary of the logic for color-coding and recommendations offered has been previously summarized  [17]  and is presented in Multimedia Appendix 1. The color-coding was based on the Canadian asthma guidelines for symptom management  [1]. An email alert was sent to patients under the following conditions: (1) when suboptimal asthma control was identified by the system and the participant indicated they did not initiate activities outlined in their action plan; (2) if the action plan was updated by the nurse as prescribed by the patient's physician; and (3) if they had not logged in for at least seven days.
Asthma Control at 6 Months Asthma control at 6 months was evaluated by examining potential overuse (yes/no) of rescue fast-acting bronchodilators (FABA; ie, beta 2-agonists) based on units dispensed for prescriptions as recorded in the provincial drug database that covers drugs dispensed for individuals who are provincially insured, medical services provided, emergency department (ED) visits, and hospitalizations. Excessive use of FABA was chosen because it is associated with an increased risk of hospitalization and asthma mortality  [22]. Based on a previously validated algorithm, asthma was classified as poorly controlled if the sum of the quantity for all FABAs dispensed was >500 doses of salbutamol 100 mcg, 2 inhalations at a time, or the equivalent for other FABAs in the last 6 months of follow-up  [1] , or the participants visited an ED for a pulmonary-related problem in the last 6 months.
Asthma-Related ED Visits or Hospitalizations Asthma-related ED visits or hospitalizations were extracted from the Quebec provincial insurance database using validated algorithms  [34]. Information on the date, type, provider, and location (eg, inpatient, emergency, clinic) for all fee-for-service medical services (~86% of all services)  [35]  is available for all Quebec residents. All outcomes were collected at 3 months (halfway) and 6 months (end) with follow-up 9 months later to evaluate persistent effects. Questionnaires were administered in the clinic at baseline and via mail thereafter.
The clustering effect was at the level of the patient to account for multiple observations on the same person over time. Mixed-effects linear regression  [36]  modeling was used to estimate the difference in asthma quality of life between groups. For both analyses, patient was the unit of analysis. An auto-regressive by a degree of 1 (AR(1)) correlation structure was used for the asthma control outcome, and compound symmetry (CS) correlation structure was used for the asthma quality of life outcome to account for multiple observations for the same patient  [36]. Both types of analyses were performed testing the effects of time, intervention, and an interaction between time and intervention (as fixed effects in the case of mixed-effects models). Analyses were conducted with SAS version 9. 3 (SAS Institute Inc) using PROC GENMOD (binary outcome), and PROC MIXED (continuous outcomes).
Models were adjusted for number of asthma medications, sex, age, education level, and self-reported health. Sensitivity analyses were conducted to evaluate the effects of missing data by imputing missing data using the Markov chain Monte Carlo method  [37]  with relative efficiency of 98% in SAS (PROC MI, PROC MIANALYZE). Secondary analyses were conducted to evaluate the mediating effects of depressive symptoms (PHQ), self-efficacy, beliefs about asthma medication (BMQ), and asthma control (ACT). In addition, the MAQLQ was added to the model with poorly controlled asthma as the outcome and asthma control status for the model with MAQLQ as the outcome. Furthermore, the proportion of individuals in each group who achieved a minimal clinically important difference (MCID) between follow-up evaluations on self-report measures was also examined.
Previous work has shown that self-reported asthma control often overestimates the effect of interventions  [41]. Our study was the first to examine the impact of a Web-based self-management program on asthma control independent of participant reporting  [12]. We used a composite measure of control based on administrative data and an algorithm for overuse of rescue medication and ED use. While none of the previous studies examined the overuse of rescue medication as an outcome, they have evaluated the impact on ED visits. Similar to our study, Rasmussen et al  [14]  found no difference in ED visits between the intervention and control groups. Unlike our investigation that showed an association between self-efficacy, depression, and beliefs about medications with asthma-related quality of life, none of the previous studies to our knowledge examined these mediating effects as possible mechanisms by which Web-based self-management interventions enhance outcomes  [12].
Acknowledgments This study was supported by a  Canadian Institutes of Health   Research operating grant  ( CIHR 89859 ,  217090 ,  204847 ), a  Career Award for SA  from the  Fond de Recherche en Santé du Quebec  (FRQS # 13870 ), and a  Canadian Foundation of Innovation Medical Informatics Infrastructure Grant  ( 15649 ). The authors wish to acknowledge  Pascale Rioux ,  Danielle Beaucage , and  Dr Ron Olvenstein  for their helpful input in the implementation of MAP and study recruitment.
Acknowledgments: The authors are grateful to  Bernard Paquette  for fruitful discussions and help during CBE runs,  Éric Breton  and  Gabriel Laliberté  for technical help with the experimental setup. This work was supported financially by  Natural Sciences and Engineering Research Council of Canada (NSERC) ,  Canadian Fundation for Innovation (CFI) ,  Fonds de Recherche Nature et Technologies (FRQNT) , and  Nano-Québec. The authors would like to thank the  Deanship of Scientific Research at King Saud University  for funding the Research Group No. RGP-1436-014  ( B Ilahi ).
For example, integration of certain dysregulated miRNAs into gene networks established from ACC omics datasets revealed their potential role in specific signaling pathways in adrenocortical cancer  (51). A new intricate dimension has been added to miRNA regulation since it was discovered that miRNAs are themselves targeted by regulatory RNA species  (52). Recent studies identified competing endogenous RNAs (ceRNAs) or natural miRNA sponges that titrate miRNA availability  (53). Such miRNA sponges bind miRNAs and competitively sequester them from their physiologically relevant targets. This class of sponges includes endogenously transcribed pseudogenes, long non-coding RNAs (lncRNA), and recently discovered circular RNAs. They may act in large complex networks in conjunction with miRNAs to regulate protein levels.
Figure6. Carbon budget of the mesocosms with time (µM C). (a) Evolution of time-integrated gross primary production (GPP), C export in sediment traps (Cexp); time-integrated net POC and net DOC are calculated assuming linear fits of these variables between days 5 and 23 (see Table3). (b) Budget of time-integrated data on day 23. The difference GPP -(Cexp + net DOC + net POC) was assumed to be community respiration (resp). The range of heterotrophic bacterial carbon demand (BCD) was calculated based on two hypotheses: BR = 100 % CR (BCD 1) or BR = 50 % CR (BCD 2). Standard errors are plotted from the sum of each category using propagation of errors.
Acknowledgements. Funding for this research was provided by the  Agence Nationale de la Recherche  ( ANR starting  grant  VAHINE ANR-13-JS06-0002 ),  INSU-LEFE-CYBER programme, GOPS, IRD  and M. I. O. The participation of UP and WRH was supported by the  German-Israeli Research Foundation (GIF) , project number  1133-13. 8/2011  and the MiSeq-based microbial community analysis by the  EU  project  MaCuMBA (Marine Microorganisms: Cultivation Methods for Improving their Biotechnological Applications ; grant agreement no:  311975 ) to WRH. The authors thank the captain and crew of the  R/V Alis. We acknowledge the SEOH divers service from the  IRD research centre of Nouméa  ( E. Folcher ,  B. Bourgeois  and  A. Renaud ) and from the  Observatoire Océanologique de Villefranche -sur-mer (OOV,  J.
FFigure 6. 6 Figure6. Carbon budget of the mesocosms with time (µM C). (a) Evolution of time-integrated gross primary production (GPP), C export in sediment traps (Cexp); time-integrated net POC and net DOC are calculated assuming linear fits of these variables between days 5 and 23 (see Table3). (b) Budget of time-integrated data on day 23. The difference GPP -(Cexp + net DOC + net POC) was assumed to be community respiration (resp). The range of heterotrophic bacterial carbon demand (BCD) was calculated based on two hypotheses: BR = 100 % CR (BCD 1) or BR = 50 % CR (BCD 2). Standard errors are plotted from the sum of each category using propagation of errors.
To further investigate the link between Setdb1 and Ankrd1 functions, we analysed the expression of Ankrd1-related genes in Setdb1 knockdown conditions. We thus checked the expression of the Ankrd1 partner Titin  [41]  and the Ankrd1 target Mmp13  [61]. Interestingly, our RNA-seq data showed that the Titin Figure  6  Wnt3a changes occupancy of Setdb1 at certain target gene promoters. (a) Setdb1 genome-wide recruitment is reduced after Wnt3a stimulation. ChIP-seq was performed in proliferating C2C12 myoblasts non-treated (Control) or treated with Wnt3a (Wnt3a). Graphic presents average Setdb1 binding density of genomic regions surrounding (±5 kb) Setdb1-binding sites (as in Figure  2a , FDR o1%, fourfold enrichment over the input and P-value o10 -5 ). Setdb1 occupancy and input density are plotted as average of reads density (every 50 bp) and normalised to total number of reads.
(e) Wnt3a increases Ankrd1 expression in proliferating primary and C2C12 myoblasts. Cells were untreated or stimulated with Wnt3a protein for 24 h (primary myoblasts) and 50-72 h (C2C12 myoblasts). Relative mRNA expression analysis of Ankrd1 was performed. Data are represented as fold change relative to untreated cells and normalised to CycloA and TBP. Data are presented as mean ± s. e. m. of three independent experiments. For significance Student paired t-test was applied. *P-values o0. 05 and are considered significant. (f) Model of Wnt3a-dependent nuclear export of Setdb1 and subsequent gene activation. In myoblasts (left) Setdb1 is located in the nucleus, where it occupies its target genes, such as Ankrd1, and represses their transcription by methylating H3K9. Hereby, interaction with other proteins are likely and require further investigation.
Titin is a Ankrd1 partner within the mechanosensory signalling complex in the sarcomere  [41] , and Mmp13 expression is negatively regulated by Ankrd1 as a transcriptional co-repressor  [61]. MMP13 being itself recently shown to play an important role in the muscle repair process, and blockade of MMP13 expression in myoblasts resulted in a delay in differentiation  [80]. These data further shed light on the functional link between Setdb1 and the 'Ankrd1 pathway'. In conclusion, we demonstrated for the first time the subcellular relocalisation of an essential epigenetic modifier by the canonical Wnt signalling as a mode of gene regulation. It will be interesting to study whether Wnt-dependent relocalisation of Setdb1 is a general mechanism in proliferating and differentiating cells. If the localisation of an epigenetic modifier, rather than its changed catalytic activity or expression, plays a crucial role in cell fate, targeting its subcellular localisation could offer a new pharmacological and therapeutic approach for multiple pathologies.
Microscopy was performed using the Axioplan 2 (Zeiss). Images were taken with the Cool Snap fx camera (Photometrics) and analysed with Metamorph software. Confocal microscopy was performed using the LM710 microscope (Zeiss, Marly le Roi, France). Confocal images were analysed with ZEN 2011 software. Light microscopy was performed using the Leica DMIL LED microscope. All images were processed with Ima-geJ software (http://rsbweb. nih. gov/ij/) to identical contrast and brightness.
7  [84]. For bound genes, we used GREAT software (v3. 0). Plots were generated with ngsplot package  [85]. Genomatix software was used for Gene Ontology analyses. Hypergeometric test has been performed in R. RNA purification and library construction for RNA-seq RNA was isolated as described above. Polyadenylated messenger RNA was purified from 1 μg RNA and the library was generated using the TruSeq stranded mRNA library prep Kit, set A and B (Illumina; #RS-122-2101 and #RS-122-2102). The obtained directional libraries were controlled by Bioanalyzer DNA1000 Chips (Agilent; # 5067-1504) and quantified by spectrofluorimetry (QuantiT High-Sensitivity DNA Assay Kit, #Q33120; Invitrogen).
Sequencing and bioinformatic analysis of RNA-seq Sequencing was performed on a HiSeq 2500 (Illumina) in a 51 bases single read using a HiSeq SR Cluster kit v4 cBot HS (Illumina; # GD-401-4001) and a HiSeq SBS kit v4 HS 50 cycles (Illumina; # FC-401-4002). Sequences were demultiplexed using the Illumina pipeline (Gerald, included in CASAVA version 1. 8) giving FASTQ formatted reads. Those reads were cleaned from adapter sequences and sequences of low quality using an in-house programme (https://github. com/baj12/clean_ngs). Sequences with a minimum length of 25 nucleotides were considered for further analysis. Tophat (version 1. 4. 1. 1, default parameters) was used to align to the reference genome (mm9). HTseq-count (parameters: -m intersection-nonempty, -s yes, -t exon) was used for counting genes  [86, 87].
Discovery | www. nature. com/celldisc than 0. 05 (*) were considered significant. P-values less than 0. 01 are marked as **. Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation: PONTIS Julien, 2016, http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?token= edkvkumqdzwbdgp&acc=GSE70070.
Acknowledgements We thank  E Boyarchuk ,  C Mozzetta ,  PA Defossez ,  A Polesskaya ,  C Rougeulle ,  S Polo ,  M Ameyar-Zazoua ,  V Joliot ,  J Weitzman ,  V Lallemand-Mezger ,  S Cooper ,  G Velasco ,  JF Ouimette  and  C Vallot  for critical reading of the manuscript. We are grateful to  Catherine Dargemont  for discussion,  Hansol Lee  ( Incheon, Korea ) for sharing information,  Yoichi Shinkai  ( Saitama, Japan ) for Eset KO ES cells,  Hidenori Ito  ( Aichi, Japan ) for the Ckm antibody and  Jeffrey M Davidson  ( TN, USA ) for Ankrd1 expression plasmid. We thank  O Faklaris ,  A Jobart-Malfait ,  X Baudin  and  V Contremoulins  from the imaging facility ImagoSeine at the  Jacques Monod Institute (Paris, France ) for precious help with confocal microscopy, image processing and analysis.
We thank  C Proux ,  JY Coppée ,  MA Dillies  and  H Varet  from ' Transcriptome and EpiGenome ' facility at the  Pasteur Institute (Paris, France ) for statistical/technical advice. We thank the  Cochin Institute Imaging Facility (Paris, France)  for fibre assay image acquisition, image processing and analysis. Work in the  Ait-Si-Ali lab  was supported by the  Association Française contre les Myopathies Téléthon  ( AFM-Téléthon );  Institut National du Cancer (INCa) ;  Agence Nationale de la Recherche (ANR) ,  Fondation Association pour la Recherche sur le Cancer (Fondation ARC) ;  Groupement des Entreprises Françaises pour la Lutte contre le Cancer (GEFLUC) ;  DIM Stem Pôle ,  Fondation Bettencourt-Schueller ; CNRS;  Université Paris Diderot  and the ' Who Am I?' Laboratory of Excellence  # ANR-11-LABX-0071  funded by the  French Government  through its 'Investments for the Future' programme operated by the  ANR  under grant # ANR-11-IDEX-0005-01.
Work in the Le Grand lab was supported by the  INSERM, CNRS ,  ANR - Jeunes Chercheurs  project  RPV13010KKA  and  AFM-Téléthon. SB was a recipient of fellowships from  Fondation ARC  and  Mairie de Paris , JP was recipient of the  Ministère de la Recherche  and  Fondation ARC  PhD fellowships, followed by a Who Am I? Labex 2014 Transition post-doc fellowship. AR was supported by an  ANR  post-doc fellowship. ES was recipient of a Who Am I? Labex 2014 post-doc fellowship followed by an  AFM-Téléthon post-doc  fellowship.
Wnt3a-mediated nuclear export of Setdb1 20 Cell 20 Discovery | www. nature. com/celldisc than 0. 05 (*) were considered significant. P-values less than 0. 01 are marked as **. Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation: PONTIS Julien, 2016, http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?token= edkvkumqdzwbdgp&acc=GSE70070.