dataesr/scientific-paragraphs-categorization huggingface dataset:
Accordingly, mean and 95 percentile exposure levels (p95) were computed, and risk characterization was performed for average and high exposure levels. To compare dietary exposure levels with the respective ADIs which are expressed per kg body weight, an average body weight of 72. 8 kg was adopted for the urban population since it was the average weight of the participants in the food consumption survey  (Nasreddine et al. 2010 ) and an average body weight of 73. 6 kg for the rural population  (Reshmany 2010). Dietary exposure levels at both the LB and UB scenarios were calculated using the Statistical Analysis Package for Social Sciences, version 18. 0 (SPSS Inc. , Chicago, IL, USA). Dietary exposure levels were first expressed in micrograms of residue per kilogram of body weight per day (μg/kg bw/d), then as a percentage of the ADI in order to characterize the chronic risk.
In the urban diet, the quantified residues' levels ranged between 10. 3 and 158. 6 μg/kg of food, whereas the quantified residues' levels in the semi-rural diet ranged between 10. 7 and 208 μg/kg of food. All the detected substances were authorized for agricultural purposes in Lebanon during the sampling period (2010), with the exception of the five POPs (Ministry of Environment (Lebanon) 1998). Lindane was detected in a composite sample of Bpasta & bulgur,^and DDD,pp. was quantified in another composite sample of Bpasta & bulgur^(15 μg/kg) from the semi-rural diet. Similarly, Dieldrin was detected in two composite samples (Bcanned vegetables^and Bcooked green leafy vegetables^) and quantified in one composite sample Although MRLs do not directly apply to composite samples and mixed dishes, the residue levels obtained in this study have been compared to the MRLs of the corresponding raw commodities, derived from the European Union Pesticide Database (European Commission 2010).
3 and 24 % in the urban and semi-rural diets, respectively. It is important to note that, since pesticide residues were not detected in any sample of beverages in the present study, the use of the UB approach may particularly overestimate exposure levels, given the high intake levels of beverages per day and the attribution of LOD and LOQ values to the undetected or unquantified results. As such, the UB dietary exposure was recalculated, without considering the beverages (data not shown). With this scenario, the mean estimated daily exposure to Dieldrin was found to be close to half   (JMPR 2001 (JMPR , 2008) )  rather for the specific sub-residues such as p,p'-DDD the ADI in both Beirut and the semi-rural area of Kesrwan and to only exceed the ADI under the 95th percentile exposure level in the semi-rural setting (124 % of the ADI).
2008 ) (Ministry of  Environment (Lebanon) et al. 2005; Hernandez et al. 1994). The consumption of animal-based foods is estimated at 355. 4 g/person/day and 381. 87 g/day in Beirut and Keserwan, respectively, thus representing, on a weight basis, 26. 5 and 24. 3 % of the urban and semi-rural diet (excluding beverages). The potential degree by which the intakes of OCs were underestimated in this study may be appraised when reviewing data published by other TDSs. For instance, the TDS conducted in China  (Zhou et al. 2012)  showed that 60 % of the daily intake of HCH was provided by meat and aquatic foods, against only 40 % by plant-based foods. Similarly, in the French TDS  (Nougadère et al. 2012) , 100 % of the intake of Lindane was provided by animal-based foods such as eggs, meat, poultry, and games.
Acknowledgments The authors would like to thank  Ms. Laila Itani  for her help in statistical analyses and  Ms. Jennifer Ayoub  for her help in the preparation of the manuscript; the study received funding from the  University Research Board  of the  American University of Beirut  and from the  World Health Organization (RPPH). 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.
Transcriptome Reconfiguration Induced by Cell Dissociation and Growth Factor Supplementation We used rabbit-specific gene expression microarray  (Jacquier et al. , 2015)  to analyze the expression of approximately 13,000 genes in CKF-4, CKF-8, AKF-5, AKF-20, AKSL-4, AKSL-8, AKSL-20, AKSF-19, AKSF-26, AKSgff-3, and AKSgff-62 (Gene Ontology accession number GEO: GSE79195). Given the inherent instability of CKL cells, they were not included in the transcriptome analysis. The gene expression profiles of the 11 aforementioned cell lines were compared with those of the ICM (mid-blastocyst, E4) and epiblast (expanded blastocyst, E6). Hierarchical clustering of normalized data (39 samples) resulted in three large clusters (Figure  3A ): (1) E4-stage ICM and E6-stage epiblast; (2) rbESCs lines derived and propagated after partial dissociation with collagenase (CKF); and (3) rbESCs lines derived and propagated after single-cell dissociation with Accutase (AKF, AKSF, AKSL, and AKSgff).
Thus, in vitro culture and dissociation methods were the two main sources of difference among the 39 samples analyzed. The third cluster, comprising 27 samples, is subdivided into two smaller clusters containing all cell lines derived in the absence (FGF À ) and presence (FGF + ) of FGF2 supplementation, respectively. To investigate this latter partition further, we built a PLS-DA model using the ropls package  (Thevenot et al. , 2015)  (Figure  3B ). This analysis identifies two directions in space segregating ''FGF + '' and ''FGF À '' samples. R2Y and Q2Y are PLS-DA metrics allowing the estimation of the accuracy of the model. We see that we have (legend continued on next page) high values for R2Y and Q2Y (these two metrics have values in the range of [0; 1]). Moreover, whatever the substitution is made between the two classes of the samples, we cannot find a better model than the one we initially proposed (all R2 and Q2 metrics obtained after substitution have a lower value than the one obtained with the initial classification: gray line for R2 and black line for Q2).
01; fold change <0. 5 or >2) from the compendium and annotated them according to the Ensembl Ocu database (Ensembl Genes 75, OryCun2. 0). The two most divergent samples were ICM and CKF cells (5,771 differentially expressed probe sets), and the two closest were AKSL and AKSgff (123 differentially expressed probe sets) (Figure  3C ). Pairwise comparison revealed that the pluripotency genes Pou5f1 (Oct4), Nanog, and Prdm14, the LIF signaling genes Il6st (gp130) and Jak1, and FGF and Clnd6 genes were upregulated in AKF cells compared with CKF cells (Figure  3D  and Table  S1 ). Conversely, Hox and Pax genes were downregulated in AKF cells compared with CKF cells. Thus, in the presence of FGF2, singlecell dissociation reinforced pluripotency gene expression, whereas partial dissociation reinforced lineage-specific gene expression.
ACKNOWLEDGMENTS We thank  Anaı ¨s Vitorino Carvalho  for microarray probe annotation. This study was supported by research grants from the  Agence Nationale de la Recherche  (ANR; projects PLURABBIT no. PCS-09-GENM-08  and  ORYCTOGENE  no. ANR-12-RPIB-0013 ),  European Cooperation in Science and Technology (COST) Action  ( Rabbit Genome Biology  [RGB]-Net no. TD1101 ),  HyPharm, Region Rhone-Alpes  ( ADR CIBLE 2010  project no. R10065CC  to Y. T. ),  Infrastructure Nationale en Biologie et SanteINGESTEM  ( ANR-11-INBS-0009 ),  Infrastructure Nationale en Biologie et Sante ĆRB-Anim  ( ANR-11-INBS-0003 ),  IHU-B CESAME  ( ANR-10-IHUB-003 ),  LabEx DEVweCAN  ( ANR-10-LABX-0061 ),  LabEx CORTEX  ( ANR-11-LABX-0042 ) of the  University of Lyon  within the  program Investissements d'Avenir  ( ANR-11-IDEX-0007 ), and  Fondation pour la Recherche Medicale  ( FRM SPE20140129375 ) to P.
6 mm Â 50 mm) from 5 to 400 ppm. The mobile phase was 73:27 15 mM NH 4 OH/(NH 4 )3PO 4 (pH 10):acetonitrile at a rate of 1 mL/min. The injection volume was 10 mL, and the wavelength was 234 nm. Mass and percentage loading were calculated from the concentration data. The diameters of unloaded and doxorubicin-loaded microspheres were measured by using an AxioZoom V. 16 motorized stereo zoom microscope with a Plan NEOFLUAR Z 1Â/0. 25 free working distance 56 mm objective and an AxioCam high-resolution cooled camera (Zeiss, Thornwood, New York). Diameter measurements were calculated by using AxioVision SE64 measurement software (Zeiss). For each measurement group, the diameter of at least 200 mm was determined. For determination of elution, doxorubicin-loaded microspheres were placed in one of seven flow cells of a CE 7smart USP 4 system (Sotax, Westborough, Massachusetts).
85). [12] Patients were seated in a custom chair with hips at 130°and knees at 90°and noncompliant straps securing the hips and chest. Force was measured via force transducer (SBB 200 kg Tempo Technologies, Taipei, Taiwan) connected by noncompliant strap to the ankle, sampled at 2000 Hz and analyzed using Labchart 8 software (ADInstruments, Bella Vista, Australia). Torque was calculated as force measured by the force transducer multiplied by the length of the lever arm. The test consisted of stages of 10 intermittent submaximal isometric contractions (5-s on/5-s off) with neuromuscular evaluations before the QIF-test, immediately after each stage and immediately after task failure. The neuromuscular evaluation was composed of isometric maximal voluntary contractions (MVCs) with femoral nerve magnetic stimuli delivered during MVCs and at rest.
Magnetic stimulation (FNMS) was delivered via 2 Magstim 200 stimulators (Magstim, Whitland, UK) connected by Bistim module and a 45-mm figure-eight coil. Submaximal target torques started at 10% MVC for the first stage and increased by 10% MVC per stage until task failure. Target torque levels were identical for a given patient throughout the intervention (i. e. , as a percentage of T0 MVC). Peak MVC and evoked torques in relaxed muscle and maximal voluntary activation were also calculated. In addition to pre-post changes for each test, data from the 10% to 40% MVC stages were analyzed because they were completed by all patients for all tests. Participant adherence is reported as the percentage of scheduled training sessions completed. Muscle damage 24 hours after neuromuscular and physiological assessments (incremental cycling, fatigue, and strength tests) was assessed from serum creatine kinase concentrations.
Statistical analysis Power assessment for the primary outcome (VO 2 peak) was based on results from Olsen et al. [8]  To detect a minimum of 20% difference from T0 to T24 between groups (CG and TG), assuming a of 5% and power of 90%, 12 patients were required per group. Statistical analyses were performed with Statistica (version 8; StatSoft, Tulsa). Assumptions of normal data distribution and variance homogeneity were verified by Shapiro-Wilk and Levene's tests, respectively. The assumption of sphericity was assessed with Mauchly's test, and in the case of significant violations, the Greenhouse-Geisser correction was applied. Twoway (Group Â Time) repeated-measures ANOVAs were used to analyze changes between TG and CG at each time point. Post-hoc analyses were performed by the Bonferroni multiple comparison procedure.
Acknowledgments The authors sincerely acknowledge all FSHD patients for their participation. They gratefully acknowledge technical support from  Régis Bonnefoy ,  Marie Pierre Blanc , and  Dominique Gouttefangeas  and clinical research assistants  Arnaud Garcin  and  Karine Ferraud  for completing the documents necessary for clinical trial authorization. They also sincerely acknowledge  Drs Emmeline Lagrange ,  Célia Boutte ,  Christophe Vial ,  Philippe Petiot ,  Alain Furby , and  Pascal Edouard  for performing medical inclusions.
This study was supported by the  Association Française contre la Myopathie (AFM). The funding source had no role in study design, data collection, data analysis, data interpretation, or writing of the report. Landry- Cyrille Bankolé  was supported by a doctoral research grant from  Örebro University  and by the  Association Française contre la Myopathie (AFM). John Temesi  was supported by a doctoral research grant from the  Rhône-Alpes Region. The authors have no conflicts of interest to disclose.
Scale bar, 5 mM. (c) U2OS cells were electroporated with either a nontargeting siRNA (siScr) or two siRNAs directed against SGK1 (siSGK1-1 and siSGK1-2) and kept in serum-free medium for further 24 h before serum refeeding in the presence of 5-FUrd. Thirty minutes after serum addition, cells were fixed and analysed by indirect immunofluorescence using antibodies specific to human KDM4A (panels 1) and Pol-I (panels 2); nuclear DNA was stained by DAPI (panels 3). Scale bar, 5 mM. transformation and cancer cell survival, as for example, a B35% reduction in Pol-I transcription in Em-Myc lymphoma cells resulted in induction of apoptosis as a consequence of immediate nucleolar stress, even before ribosome insufficiency takes effect on biosynthetic capacity  26. Our data also bring important insights into the precise step of rDNA transcription which requires KDM4A.
Expression plasmid encoding myc-tagged wild-type PTEN (pcDNA3-PTENWT) was a gift from Evelyne Goillot (ENS Lyon, France). Cells were seeded on glass coverslips and transfected with either empty pCDNA3, pcDNA3-PTENwt or pcDNA3-PTENmut using jetPEI with a ratio of 1 mg DNA for 2 ml of jetPEI following the manufacturer's recommendation (Ozyme). RNA labelling in cells and rRNA analysis. Labelling of RNA in cells (B70% confluent or B50% for starved/refed) and RNA analysis was performed essentially as described 44 using 10 mCi 3 H-uridine for B0. 2-0. 4 Â 10 5 cells per well of a six-well plate. RNA was extracted (Pure Link RNA Mini kit, Life Technologies). 2 mg of 3 H-labelled total RNA was run on a 1% formaldehyde agarose gel at 120 V for 95 min in 1 Â MOPS, blotted onto Hybond-N membrane (Amersham), crosslinked (ultraviolet cross-linker; UVP), analysed by tritium imaging using Fuji Tritium image plate (or following PerkinElmer En 3 Hance spray, exposed to Kodak Biomax XAR film at À 80°C) and then quantified using Aida software.
The s. d. was calculated from three independent experiments. In situ RNA labelling was performed using 5-Fluorouridine (5-FUrd, Sigma). Cells were incubated with 1 mM 5F-Urd for 30 min before fixation with 4% paraformaldehyde in PBS, for 15 min at 4 °C. 5-FUrd incorporation was analysed by immunofluorescence using anti-BrdU antibodies (BU-33, Sigma). All the staining procedure was performed at 4 °C, in the presence of 0. 4 U ml À 1 RiboGuard RNAse inhibitor (Epicentre). Quantification of fluorescence levels was done on B100-200 cells per slide using home-developed macros in Image J software (National Institutes of Health) and analysed using the R open source software R Core Team (2014), (http://www. R-project. org/). ChIP and sChIP assays. Cells were grown until 70% confluent, crosslinked with formaldehyde (final concentration 1%) for 10 min and the cross-linking was stopped by addition of glycine (final concentration 0.
Cells were then incubated at 4 °C overnight with the indicated primary antibodies: Rabbit polyclonal anti-JMJD2A (Bethyl A-300-861-A; 0. 5 mg ml À 1 ), Rabbit polyclonal anti-KDM4A antibodies (Sigma, HPA007610, 0. 5 mg ml À 1 ), Rabbit polyclonal anti-HA (Cell Signaling C29F4, 1 mg ml À 1 ), RPA 194 Santa Cruz SC-48385 1 mg ml À 1 , mouse monoclonal anti-UBF (SC-13125 1 mg ml À 1 ), mouse monoclonal anti-BrdU 2 mg ml À 1 (BU-33, Sigma), mouse monoclonal anti-myc antibodies (9E10, Santa Cruz). AlexaFluor-conjugated secondary antibodies were purchased from Fisher Scientific. Observations were carried out with a fluorescence microscope (DM5000; Leica, Wetlar, Germany) equipped with a cooled charge-coupled device camera, and images were acquired using the MetaMorph imaging system (Universal Imaging Corp.
, West Chester, PA). For Z-stacks acquisition (Fig. 1b ), images were collected with a DM6000 Leica microscope equipped with semrock filters, a PiFoc piezofocus device (Physic Instrumente), and a CollSnapHQ2 camera (Roper Scientific), controlled by MetaMorph software (Universal imaging Corp. ). Five Z-sections at 0. 2 mm spacing were projected onto a single plan. Box-and-whisker plots of quantification of 5-FUrd staining were obtained with the R open source software R Core Team (2014), (http://www. R-project. org/). They show the median, the 25 and 75% quantiles, as well as outliers (outliers are identified by not being in the range [25%Quantile À 1. 5 Â InterQuantiles; 75%Quantile þ 1. 5 Â InterQuantiles] where interQuantiles ¼ 75%Quantile À 25%Quantile). These representations have to be accompanied by statistical analysis of the comparison between the two populations.
Sterols composition The sterol composition was determined using a Varian 3800 instrument (Varian Inc. , Walnut Creek, CA, USA) equipped with a VF-1ms column (30 m × 0. 25 mm i. d. ) and using helium (flow rate 1. 6 mL/min) as the carrier gas. The column temperature was isothermal at 270 • C and the injector and detector temperatures were both 300 • C. The injected quantity was 1 L for each analysis. The data were processed using Varian Star Workstation v 6. 30 (Varian Inc. , Walnut Creek, CA, USA).
Data were acquired using Xcalibur software (version 2. 1; Thermo Fisher Scientific, San Jose, CA). The instrument was operated in positive data-dependent mode. Resolution in the Orbitrap was set to r ϭ 60,000. In the scan range of m/z 300 -1800, the 20 most intense peptide ions with charge states Ն2 were sequentially isolated (isolation width, 2 m/z; 1 microscan) and fragmented using collision induced dissociation. The ion selection threshold was 500 counts for MS/MS, and the maximum allowed ion accumulation times were 200 ms for full scans and 50 ms for collision induced dissociation-MS/MS in the LTQ. Target ion quantity for FT full MS was 1e6 and for MS/MS it was 1e4. The resulting fragment ions were scanned at the "normal scan rate" with q ϭ 0. 25 activation and activation time of 10 ms.
Dynamic exclusion was active during 30 s with a repeat count of 1. The lock mass was enabled for accurate mass measurements. Polydimethylcyclosiloxane (m/z, 445. 1200025, (Si(CH 3 ) 2 O) 6 ) ions were used for internal recalibration of the mass spectra. Protein Identification and Data Validation-Raw data files were converted to MGF using Proteome Discoverer software (version 1. 2; Thermo Fischer Scientific, San Jose, USA). Precursor mass range of 350 -5000 Da and signal to noise ratio of 1. 5 were the criteria used for generation of peak lists. In order to identify the proteins, the peptide and fragment masses obtained were matched automatically against the Swissprot_2013. 01 database (66153 entries). MS/MS ion searches were performed using MASCOT Daemon and search engine (version 2. 3; Matrix Science, London, UK).
The parameters used for database searches include trypsin as a protease with allowed two missed cleavage, carbamidomethylcysteine (ϩ57 Da), oxidation of methionine (ϩ16) and N-terminal protein acetylation (ϩ42) as variable modifications. The tolerance of the ions was set to 5 ppm for parent and 0. 8 Da for fragment ion matches. Mascot results from the target and decoy databases were incorporated to Scaffold 3 software (version 3. 6, Proteome Software, Portland, OR). Peptide identifications were accepted if they could be established at greater than 95. 0% probability as specified by the Peptide Prophet algorithm  (36). Peptides were considered distinct if they differed in sequence. Protein identifications were accepted if they could be established at greater than 95. 0% probability as specified by the Protein Prophet algorithm and contained at least two identified peptides (FDR Ͻ 1%).
Label-free Protein Quantification-Scaffold 3 Qϩ software was employed (version 3. 6, Proteome Software, Portland, USA) using spectral count quantitative module. All proteins with greater than two peptides identified in SwissProt database with high confidence were considered for protein quantification. To eliminate quantitative ambiguity into protein groups, we ignored all the spectra matching any peptide which is shared between proteins. Thereby, quantification from normalized spectral counts was carried out on distinct proteins. Student's t test was done to characterize changes between two samples. Statistically significant differences were considered for p Ͻ 0. 05. Gene Ontology-The Uniprot accession numbers were submitted to the UniProt Knowledgebase (UniProtKB) and the Gene Ontology data were retrieved for all the 940 identified proteins.
The subcellular location data were used to generate a pie graph. A panel of 16 main biological functions was used to categorize the proteins and generate a pie graph. Data Repository-The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www. proteomexchange. org) via the PRIDE partner repository  (37)  with the data set identifier PXD000299. Western Blotting-Primary antibodies directed against the following proteins were purchased from Santa Cruz Biotechnologies (Santa Cruz, CA): zinc ␣ glycoprotein (dilution 1/500, sc-11358), lactoferrin (1/500, sc-52694), ␣-enolase (1/500, sc-15343), CD109 (1/500, sc-98793), myosin 9 (1/500, sc-98978), ceruloplasmin (1/500, sc-21240), Hsp105 (1/500, sc-1805). Primary antibodies directed against the following proteins were purchased from Abcam (Cambridge, England): gelsolin (1/1000, ab11081), valosin containing protein/VCP (1/ 2000, ab11433), heat shock protein (HSP) 90 ␤ (1/1000, ab82522), heat shock protein 70 (HSPA2, 1/200, ab1428), and HSPA8 (1/2500, ab1427).
The western blots were blocked with TBS-Tween 20 (0. 5%, w/v), supplemented with lyophilized low-fat milk (5% w/v). Membranes were incubated with primary antibodies under mild agitation overnight at 4 °C or for 1. 5h at 37 °C and with secondary antibodies overnight at 4 °C or for 1h at 37 °C. The peroxidase was revealed with chemoluminescent substrates and the images recorded on film or digitized with a cooled CCD camera (ImageMaster VDS-CL, Amersham Biosciences, GE HealthCare Lifesciences, Pittsburgh, PA). The intensity of the signal was quantified using the TotalLab Quant software (TotalLab, Newcastle upon Tyne, UK). Immunohistochemistry-Tissue-Tek-embedded, 10 m sections of cervix were prepared on Superfrost Plus microscope slides (Thermo Fisher Scientific) with Cryostar NX70 (Thermo Fisher Scientific), and fixed with acetone at Ϫ20 °C for 20 min.
RESULTS The Proteome of the Female Genital Tract Fluids-This study aimed to compare the proteome from the luminal fluids at two biologically significant stages of the cycle (estrus and luteal phase) from the three adjacent regions of the female genital tract; namely, the cervix, uterus and oviduct. We collected the cervical mucus originating from the inner part of the cervix only, to characterize as much as possible the secretions from the cervical epithelium. The uterine and the oviduct fluids were collected from gentle flushing with a very limited volume of buffer in order to analyze a fluid being as close as possible to the native fluids. The combination of in-solution and in-gel digestion MS data from the fluids originating from the female tract yielded in the total identification of 940 proteins.