dataesr/scientific-paragraphs-categorization huggingface dataset:
g Heatmap of genes within the "mitosis" GO term differentially expressed between HDF N and HDF 87 y (Supplementary Data 2). h Heatmap of SASP and senescence-associated (CDKN1A, LMNB1) genes differentially expressed between HDF N and HDF 87 y (Supplementary Data 4); 2logFCs in red indicate genes behaving differently from expected  36, 37. i Heatmap of senescence core signature genes differentially expressed between HDF N and HDF 87 y (Supplementary Data 5); 2logFCs in red indicate genes behaving differently from expected  37. In all heatmaps, 2logFC cutoff value < -0. 5 and >0. comparison with 3. 2% in neonatal senescent cells (Fig. 7f ). Thus, aneuploidy appears as an overt feature in elderly senescent cells, especially if we consider that only 3 out of 23 chromosome pairs were measured. To investigate whether FoxM1 repression is responsible for this difference, we next FACS-sorted SA-β-galpositive cells from siFoxM1-depleted neonatal cell cultures and from octogenarian cell cultures expressing FoxM1-dNdK (Fig.
FSC-width plot. The signal was detected using the APC-A channel. The relative β-galactosidase activity was inferred from the median fluorescence intensity of the population. The sorting gates were designed accordingly to the respective auto-fluorescent control. Cells were sorted directly into MEM with 15% FBS and seeded in Superfrost™ Plus microscope slides for subsequent FISH analysis. Analysis of FACS data was done using FlowJo v10 software (TreeStar, Inc. , Ashland, OR). Immunostaining. Fibroblasts were grown on sterilized glass coverslips coated with 50 µg/ml fibronectin (F1141, Sigma-Aldrich, MO, USA). Cells were fixed in freshly prepared 4% paraformaldehyde in PBS for 20 min. Following fixation, cells were rinsed in PBS and permeabilized in PBS + 0. 3% Triton-X100 for 7 min. Cells were next blocked in 10% FBS in PBS-T (PBS + 0.
05% Tween-20) for 1 h and then incubated overnight at 4 °C with primary antibodies diluted in PBS-T + 5% FBS as follows: rabbit anti-53BP1 (4937, Cell Signaling Technology, MA, USA),  (20-25) were imaged every 2. 5 min for 2-3 days, using a ×20/0. 3 numerical aperture (NA) A-Plan objective. Stitching of neighboring fields was done using the plugin "Stitch Grid" (Stephan Preibisch) from ImageJ/Fiji software. Live-cell and fixed-cell correlative microscopy. Eighty-seven-year-old fibroblasts expressing H2B-GFP were grown in µ-Slide 2 Well ibiTreat (Ibidi GmbH) and analyzed accordingly to the experimental layout shown in Fig. 7i. Images were acquired on a Leica DMI6000b inverted microscope (Leica Microsystems, Germany), equipped with an ORCA-Flash4. 0 camera (Hamamatsu, Japan), using the laser line 488 nm for the excitation of green fluorescent protein (GFP), and under controlled temperature, atmosphere and humidity.
Neighbor fields (60-70) were imaged every 5 min for 3-4 days, using a ×20 LD/0. 4 NA objective (Leica Microsystems). Following the long-term live-cell imaging, cells were processed for SA-β-gal assay and 53BP1/p21 double immunostaining as described elsewhere in this section, and the same neighbor fields acquired using a ×40 LD/0. 6 NA objective. LAS X software (Leica Microsystems) was used for image acquisition and analysis. Spinning-disk confocal microscopy. Four-dimensional data sets were collected with Andor Revolution XD spinning-disk confocal system (Andor Technology, Belfast, UK), equipped with an electron-multiplying charge-coupled device  Fig. 8  Positive feedback loop between aging and aneuploidy. Model summarizing the molecular basis of age-associated mitotic decline and accumulation of senescent cells induced by aneuploidy.
A GS-800 calibrated densitometer with Quantity One 1-D Analysis Software 4. 6 (Bio-Rad Laboratories) was used for quantitative analysis of protein levels. Uncropped scans of all blots in the main manuscript and supplementary figures are provided in Supplementary Fig. 11. Lentiviral plasmids. H2B-GFP  69  was amplified as a BglII-H2B-GFP-T2A-BamHI-NotI fragment. This PCR fragment was digested with BglII + NotI and ligated into pRetrox-Tight-Puro (Clontech, CA, USA) digested with BamHI + NotI, thus destroying the 5′ BamHI/BglII site, while reintroducing a BamHI site 3′ of H2B-GFP-T2A. In parallel, α-Tubulin 69 was amplified as a BglII-α-Tubulin-BamHI-NotI fragment and ligated into pRetrox-Tight-Puro digested with BamHI + NotI, again destroying the 5′ BamHI/BglII site, while reintroducing a BamHI site 3′ of α-Tubulin.
The 2 -ΔΔCt method was used to quantify the transcript levels of FOXM1, CDKN1A, MMP1, CXCL8, TSPAN13, and FAM214B against the transcript levels of the housekeeping gene (TBP). Primers were designed to span at least one exon-intron junction (Supplementary Table  3 ). Amplification was performed in a C1000 Touch Thermal Cycler (CFX384 Real-Time System, Bio-Rad Laboratories) and analyzed using CFX Manager Software (Bio-Rad Laboratories). RNA-seq and bioinformatics. RNA was isolated from mitotic human fibroblasts and validated as described above for Real-time PCR. RNA-sequencing libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/ Rat (RS-122-2201; Illumina, CA, USA) according to manufacturer's protocol. Pooled libraries were sequenced on an Illumina HiSeq 2500 (single-end 50 bp).
Raw unaligned sequencing reads (fastq-format) were deposited in the European Nucleotide Archive (ENA) under the accession number PRJEB27047. Reads were aligned to the human genome (hg19) using a splicing-aware aligner (StarAligner). Aligned reads were fragments per million (FPM) normalized, excluding low abundance genes (mean FPM > 1). Differential gene expression analysis was performed using a likelihood ratio test constructed under the R-package edgeR (v3. 14. 0 available from Bioconductor at http://www. bioconductor. org/packages/ release/bioc/html/edgeR. html). Significant differential gene expression of aged fibroblasts was defined as p-value < 0. 05 and 2logFC cutoff value < -0. 5 or > 0. 5; and in case of genetic manipulations as p-value < 0. 05, 2logFC cutoff value < -0. 5 or > 0. 5, and FDR < 0.
05. For generation of RNA-seq heatmaps, transcript counts were normalized to the sample library size. These values were subsequently scaled by gene using normalized scores or z-scores (i. e. a value of 0 corresponds to the mean gene expression of that gene across all libraries, and ± 1, ± 2, etc. represent 1, 2, etc. SDs from the gene mean). Hierarchical clustering was performed using the R library heatmap. 2. RNA-seq data represent two independent experimental replicates of each biological sample. GO term enrichment analysis of differentially expressed genes was performed using Database for Annotation, Visualization and Integrated Discovery Functional Annotation Tool v6. 7  70  (www. david-d. ncifcrf. gov). To calculate the significance of gene set enrichment, empirical p-values were generated using DAVID tool.
Acknowledgements We thank  H. Maiato ,  J. M. Cabral , and  J. Bessa  at  i3S  for critical discussions and reading of the manuscript;  P. Sampaio  and  A. Maia  for technical help with Advanced Light Microscopy. E. L. holds an  FCT Investigator Postdoctoral Grant  ( IF/00916/2014 ) from  FCT/MCTES  ( Fundação para a Ciência e a Tecnologia/Ministério da Ciência, Tecnologia e Ensino Superior ). FCT Fellowships ( SFRH/BD/74002/2010 ;  SFRH/BD/125017/2016; PD/BD/128000/2016 ) supported J. C. M. , S. V. , and  R. R. The  following project grants supported this work:  National Funds through FCT  under the project  PTDC/BEX-BCM/ 2090/2014  ;  NORTE-01-0145-FEDER-000029  funded by  North Regional Operational Program (NORTE2020)  under  PORTUGAL 2020 Partnership Agreement through Regional Development Fund (FEDER) ;  NORTE-07-0124-FEDER-000003  co-funded by  North Regional Operational Program  ( ON.
In  [8] , the authors proposed an efficient certificateless signcryption model for access control in wireless body area networks. In the registration phase, every user first generates a public key pair, and sends it to the Key Generator Center (KGC) in order to get a partial private key. Upon receiving his partial private key, the user could compute his full public key pair. As only registered user could generate this public key pair, this generation can be considered as a measure to verify the legitimacy of the user. Given that only the public key is transferred, the user's identity is hidden and anonymity is ensured. However, in their scheme they consider that all the data consumers have the same privileges. In  [9]  an efficient and certificateless scheme that exploited the generalized signcryption (CLGSC) model was proposed.
4) Computation Cost In this subsection, we compare the proposed H-CLSC scheme with the three other schemes in terms of computational overhead. As the operations on pairing, exponentiation and multiplication heavily influence the computational overhead, we only take into account these three operations. We denote TE the time consumed for one exponentiation operation, TM the time consumed for one scalar multiplication in 1, and TP the time for one pairing operation. In our proposed H-CLCS scheme, the signcryption process in WBAN client takes six multiplication operations in 1 and three pairing operations in 2. The computational cost for the H-CLCS scheme and the other authentication and authorization models are presented in Table  5. According to  [9] , to quantify the running time of the operations, the algorithms are implemented on an Intel PXA270 processor at 624 MHz installed on the Linux personal digital assistant.
A control flow cell submitted to all coupling steps without immobilized protein or with immobilized fatty acid-free BSA was used as a reference, and the specific binding signal was obtained through subtracting the background signal over the reference surface. Kinetic data were analyzed via global fitting to a 1:1 Langmuir binding model of both the association and dissociation phases for at least four SP-D concentrations simultaneously, using the BIAevaluation software (version 3. 2, GE Healthcare). Buffer blanks were subtracted from the datasets used for kinetic analysis (double referencing). The apparent equilibrium dissociation constants (KDs) were calculated from the ratio of the dissociation constant (kd) and association rate constant (ka) (kd/ka). The values provided were the means ± standard deviations (SDs) from two independent experiments.
Characterization of SP-D Binding to GP by SPR Spectroscopy SPR spectroscopy was used to further characterize the interaction between hSP-D and GP. Increasing amounts of hSP-D were injected over the immobilized GPTM. As displayed in Figure  2A , binding was dose-dependent and further kinetic analysis of the binding data yielded association and dissociation rate constants of (2. 61 ± 0. 92) × 10 6 M -1 s -1 and (3. 19 ± 0. 81) × 10 -4 s -1 , respectively, using a global fitting to a 1:1 Langmuir interaction model. The deduced apparent equilibrium dissociation constant (KD) was 0. 12 ± 0. 01 nM, indicative of a high affinity. EBOV GP is a highly glycosylated protein and the majority of the N-glycosylation sites are concentrated in the glycan cap and mucin-like domain (MLD), while sialylated O-glycans are predominantly located in the MLD.
CRD, carbohydrate recognition domain EBOV, Ebola virus (Zaïre ebolavirus specie) HA, hemagglutinin protein of IAV IAV, influenza A virus MBL, mannose-binding lectin MLV, Murine leukemia virus NCRD, recombinant trimeric neck+CRDs SP-A, surfactant protein A SP-D, surfactant protein D VLP, virus-like particle VSV, respiratory syncytial virus RESTV, Ebola virus (Reston ebolavirus specie) RFP, red fluorescent protein Funding: We acknowledge the support of the Direction Générale pour l'Armement (DGA), the Service de Santé des Armées (PDH-2-NRBC-4-B2-408), and the ARAMI association. This work used the platforms of the Grenoble ERIC-Instruct Center (ISBG; UMS 3518 CNRS-CEA-UGA-EMBL) with support from FRISBI (ANR-10-INSB-05-02) and GRAL (ANR-10-LABX-49-01) within the Grenoble Partnership for Structural Biology (PSB).
Acknowledgments: We thank  I. Bally  and  J. B Reiser  for access to the  SPR facility  and  J. P Kleman  for access to the cell-imaging platform (flow cytometer). We are grateful to  Pr. E. Ollmann Saphire  and  Dr M. Fusco  ( Scripps institute, La Jolla, USA ) for the kind gift of GP-EBOV Mayinga strain plasmids. We thank  Dr. McCormark  ( Pulmonary and Critical Care Medicine, The University of Cincinnati, Ohio, USA ) for the AP-SP-A protein and the late Pr. Jo Wright (deceased on  2012/01/11 ,  Duke University, Durham, North Carolina, USA ) for the rSP-A protein.
Immunocytochemistry and High-Resolution Microscopy Following 30 min fixation in 10% formalin (HT5014, Sigma-Aldrich), myotubes were washed three times in Dulbecco's Phosphate-Buffered Saline (DPBS; 14190169, Invitrogen) and permeabilized in 0. 1% Triton X-100 (T9284, Sigma-Aldrich). After blocking in 1% bovine serum albumin (BSA; A7906, Sigma-Aldrich), cells were incubated with primary antibodies (Suppl. Table  S1 ) for 90 min at room temperature and washed three times in DPBS. Secondary antibodies were added for 1 h with Hoechst 33342. Cells were washed three times in DPBS before acquisition. A DMI6000 (Leica Microsystems, Nanterre, France) or Eclipse-Ti (Nikon, Champigny-sur-Marne, France) wide-field microscope controlled by Metamorph software (Molecular Devices, Sunnyvale, CA, US), and equipped with digital C8484 or ORCA-R2 charge-coupled device (CCD) cameras, respectively (Hamamatsu, Bridgewater, NJ, US), was used for video-imaging and when higher spatial resolution was required.
High-Content Phenotypic Screening After fixation and immunostaining (Suppl. Table  S1 ), quantitative microscopy was performed using the Operetta HCS imaging system with a 10×/0. 3 NA objective (PerkinElmer, Courtaboeuf, France). Images were analyzed using scripts developed in Acapella software (PerkinElmer), including customized segmentation of myotubes and nuclei. Micropatterned and conventional myotubes were defined as areas positive for skeletal muscle differentiation markers fast-myosin heavy chain (fast-MHC) or troponin T and conforming to specific filters optimized for each culture system. Filters to identify nonpatterned myotubes were based on areas that are greater than a minimum intensity threshold and contain two or more nuclei. For patterned myotubes, additional stringent properties were calculated, including the min/max area, maximum orientation, minimum elongation, and min/max length of myotubes.
Images were processed and analyzed automatically using a dedicated software developed in-house that integrates the open-source ImageJ framework. 26 The image analysis tool segments myotubes in images acquired throughout time in the same well. The Fluo-4 total fluorescence intensity is measured inside each myotube and corrected for background. The total intensity is normalized to the myotube area to obtain the mean fluorescence intensity for each myotube. For data presentation, kinetic curves of calcium response are expressed as time (x-axis) versus the ratio F/F0 (y-axis), where F is the mean fluorescence intensity normalized to F0, the baseline mean fluorescence intensity measured before compound addition.
MyoScreen HCS Pipeline Development To streamline processes, quantitative image acquisition and analysis of changes in myotube morphology were implemented on the Operetta imaging system using custom Acapella scripts and just two imaging channels to identify nuclei and myotubes, as outlined in Supplemental Figure  S1A. Eleven fields per well imaged with a 10× objective ensured analysis of >5750 micropatterns/96-well plate with each pattern organizing multiple myotubes, thus providing robust statistics while maximizing throughput. Images were processed with computing on a per-micropattern basis, and data output was presented as a mean of triplicate wells. Compared to NP myotubes that are difficult to analyze individually, images of multiple horizontally aligned myotubes with standardized orientation and morphology could be segmented and analyzed without application of tedious image-processing routines, accelerating measurement of descriptors including number of myotubes, FI, mean myotube size, myonuclei per myotube, and mean fluorescence intensity of differentiation markers.
To test the validity for screening of an assay to quantify modulation of AChR clusters, the Z'-factor was calculated from 30 medium-only control wells and 30 agrin-treated wells from more than three separate CYTOOplates (data not shown). Using agrin as a reference against background and the most stable imaging parameter, namely AChR total cluster area, the average Z'-factor was >0. 4 and controls had CVs of 9-12%, indicating an assay with high sensitivity and reproducibility. These data demonstrate for the first time that human myotubes can form AChR clusters in the absence of innervation. Likely, AChRs were not observed previously due to the poor maturation status of conventionally grown human myotubes, providing further evidence for the improved biomimicry of MyoScreen myotubes. Morphologically, AChR-rich clusters in control and agrin-treated myotubes resemble plaque-stage aggregates (Fig.
MyoScreen Myotubes Are Functional for ACh-Induced Postsynaptic Transmission and Contraction In skeletal muscle in vivo, ACh activation of AChRs induces channel opening and local depolarization of the plasma membrane, igniting an action potential that spreads along and into the myofiber, triggering release of stored calcium into the myoplasm and subsequent contraction. Autonomous contractions were occasionally visible in MyoScreen myotubes, indicating spontaneous discharge of action potentials (data not shown). To test the functionality of AChRs for postsynaptic signal transmission, transient changes in intracellular calcium concentration ([Ca 2+ ] i ) were analyzed in response to stimulation by the neurotransmitter ACh, to mimic motor neuron input. To ensure maturation, calcium transients were measured by live cell fluorescent imaging of day 8-9 differentiated myotubes (male, 21 years) loaded with a calcium indicator, Fluo-4 AM.
Addition of a bolus of 20 µM ACh induced a sharp (millisecond) fourfold increase in Fluo-4 fluorescence, reflecting myotube excitation and an increase in myoplasmic Ca 2+. This was followed by a slower (seconds) decrease in Fluo-4 fluorescence to nearresting levels, which occurs during myotube contraction and relaxation, and resequestering of Ca 2+ into the sarcoplasmic reticulum (SR; Fig. 5A ). Changes in Ca 2+ flux occurred in tandem with myotube contraction and relaxation observed during simultaneous phase-contrast videomicroscopy (Suppl. Movie S1). Similar Ca 2+ kinetic data were obtained using Molecular Devices' FlexStation, which is designed for higher throughput measurements (data not shown). To verify the specificity of the ACh-triggered response, myotubes were preexposed to tubocurarine (100 µM), a competitive ACh inhibitor that binds to AChRs.
MyoScreen Secondary Assays Provide Further Functional Readouts of Compound Activity To further characterize the biological activities of CYT3818 and CYT9733, effects of the compounds were investigated on other aspects of myotube physiology, namely, AChR expression, Ca 2+ flux, and contraction. All three assays were performed using the female, 20-year-old donor and 0. 1 µM CYT3818 or 2 µM CYT9733, concentrations shown to induce maximum response in all donors (Fig. 6B ), and the effects were compared to those of the reference compound, IGF1, at 18. 75 nM. After 8 days of differentiation that included 7 days of drug treatment, myotubes treated with CYT3818 and CYT9733 showed substantially more AChR clusters (data not shown), and total AChR area increased by three-and sixfold, respectively, while IGF1 had no effect (Fig.
Meteorological data Precipitation and potential evapotranspiration are provided by the French national meteorological agency (Météo-France). The nearest meteorological station of each site was selected. Precipitation is monitored daily at 4 km to the south-east of SEOU site and 5 km to the south of the BESS site. Rain gauges are automatic tipping-bucket with a resolution of 0. 2 mm. The accuracy of rain gauges is equal to 4 % during weak precipitation, but the errors increase when pre-cipitation exceeds 150 mm h -1 (10 % accuracy)  (Civiate and Mandel, 2008) , which is rare in the area. The rainfalls are spatially homogeneous on the seasonal scale but not on the event scale  (Fores et al. , 2017). Both sites (BESS and SEOU) are mainly influenced by Mediterranean climate even if in BESS a clearer influence of the oceanic climate can be observed.
, 2010). The gravity differences relative to the reference station and the drift value are obtained using a least-square adjustment scheme with the software MCGRAVI  (Belin, 2006)  based on the inversion scheme of GRAVNET  (Hwang et al. , 2002). Parameters to be estimated are the gravity value at each station (surface and depths) and the linear drift of the gravimeter. Measurements of one station (m d ) relative to the reference station (m s ) can be expressed as follows: C f m t j s -m t i d + ν S j S i = g s -g d + D k t j -t i , (1) where C f is the calibration correction factor, m t j s and m t i d are the reference and station gravity reading at times t j and t i respectively, ν S j S i is the residuals of (m t j s -m t i d ), D k is the linear drift of the loop k, and g s and g d are the gravity values at the reference and the station.
The residuals depend on the precision of the processed data and on the robustness of the measurements strategy. For example, if a histogram of a residual is centred on 0, it suggests that the correction processes have not introduced a bias in the gravity value estimation. The dispersion of the residuals can indicate noisy measurements or non-linear drift. The shape of the histogram shows the global precision of dataset. The residuals were estimated for each dataset (Fig. 5 ) and can be used to compare the two measurement strategies. Most of the histograms display a Gaussian shape centred on zero with a small dispersion showing the good quality of the gravity readings and hence the robustness of the surfaceto-depth gravity differences ( g S2D ). However, the residuals of -8 µGal (Fig. 5a ) for the period t 1 at the SEOU site are due to an unexpected gravity jump during the survey.
As no explanation was found for the gravity jump, they are kept for data adjustment even if the dispersion of the gravity residuals increases accordingly. For the two first datasets, 90 % of residuals are comprised of 8 µGal intervals. For the last three datasets, 90 % of residuals are between -2 and +2 µGal. Residuals histograms of the long time strategy are narrower than those of the short time strategy which confirms the improvement of the field experiment strategy (Fig. 5 ). The relaxation due to transportation or non-linear drift would have induced a non-Gaussian shape of the histograms not centred on zero as seen during the second survey at the SEOU site (Fig. 5a ). We have tested in a cave the long time strategy using repeated measurement on a single station interrupted by hand transportation.
As for the data shown here, these unpublished results, show a smaller dispersion of the residuals than the one provided by the short time strategy and an unbiased mean. Gravity data after correction and drift adjustment are presented in Table  A1  in the Appendix. For the SEOU site, the g S2D values show significant temporal variations ranging from -3. 897 to -3. 914 mGal. At the BESS site, between the surface and 12 m depth, g S2D values range from -1. 523 to -1. 537 mGal. Below 12 m, gravity variations are not significant.