dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGMENTS (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. We thank the members of the team for stimulating discussions,  Jean-Michel Gibert  for critical reading of the manuscript,  Immane R'Kiki  for technical assistance,  Naïra Naouar  from the  ARTbio Bioinformatics platform (IBPS)  for the training of HG in NGS analyses, the  Bloomington Stock Center  for fly strains. This work was funded by the  Centre National de la Recherche Scientifique (CNRS) ,  Sorbonne University , and by a  Fondation ARC  grant to FP ( PJA20171206407 ). HG was funded by a doctoral fellowship from the  MESRI (Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation)  and a 4 th year doctoral fellowship from  Fondation ARC  ( ARCDOC42020020001381 ).
JD was funded by a doctoral fellowship from the  MESRI  and a 4 th year doctoral fellowship from the  Fondation pour la Recherche médicale  ( FDT20160435164 ). This work was supported by the  France Génomique national infrastructure , funded as part of the  "Investissements d'Avenir" program  managed by the  Agence Nationale de la Recherche  (contract  ANR-10-INBS-0009 ).
Thus, we pursued our analysis by searching for cassette exons that demonstrate a significant difference in the level of inclusion between MBNL1(-/-), DKO and WT hiPSC-derived myotubes. A total of 547 cassette exons were found to be deregulated between DKO and WT hiPSC-derived myotubes, among which 296 and 251 exhibited a significant decrease and increase in inclusion, respectively [FDR < 0. 05; delta percent spliced-in (PSI) > 0. 4] (Fig. 7A  and Supplementary Material, Table  S5 ). We next compared these analyses with transcriptomic data generated from DM1 hiPSC-derived myotubes (Fig. 7A ). Of the 696 missplicing events [differentially spliced exons (DSE)] observed in DM1 hiPSC-derived myotubes, 224 (32%) appeared in MBNL1(-/-) hiPSC-derived myotubes. In the same way, 254 (36%) appeared in DKO hiPSC-derived myotubes and among these, 126 were commonly mis-spliced in DM1, MBNL1(-/-) and DKO hiPSC-derived myotubes (Fig.
All the data about the enriched biological processes are detailed in Supplementary Material, Table  S6. (D) List of 30 enriched DSEs covering most of the deregulated biological processes related to skeletal muscle and identified in DKO hiPSC-derived skeletal muscle cells compared with WT. For alternative splicing analysis, exons have been numbered according to FasterDB database. The numbers of the corresponding exons are indicated in brackets (EnrichR analysis using GO Biological Process 2018 database). human pluripotent stem cells into a reasonably mature muscle cells relied on the forced expression of transcription factors such as MyoD or Pax3/7  (38). These direct reprogramming approaches aim to bypass early developmental stages by overexpressing myogenic regulators, and the cellular events occurring during differentiation remain largely unclear  (39).
The quality control of the sequencing data was evaluated as described previously  (57). The DEG between conditions was calculated with (v1. 18. 1 using R v3. 4. 1). Genes were considered differentially expressed when their adjusted P-value was <0. 05 and their|log2FoldChange|was >0. 4 (options: lfcThreshold = 0. 4, altHypothesis = 'greaterAbs'). Data are available on GEO database (GSE161029).
RNA-Seq library preparation and sequencing (TrueSeq polyA) For each sample, 100 ng of total RNA was used. mRNAs were purified using poly-T oligo from TruSeq Stranded kit (Illumina ® ) and were fragmented and reverse transcribed using the TruSeq Stranded kit following the protocol of the manufacturer. Final library was quantified using Agilent high-sensitivity DNA kit before the samples were pooled in sets of six for sequencing. A total of 2 nM of pooled libraries were denatured, and the quantity of 1. 8 pM was used for cluster generation before paired-end sequencing on an Illumina Nextseq550 (high output 2 × 150 bp run). Samples were sequenced with an average of 89 532 366 reads (paired-end) per sample. The quality control of the sequencing data was evaluated using FastQC (v0. 11. 2). The reads were trimmed using Prinseq (v0.
20. 4) (-trim-right 20) and filtered by average quality score (-trim-qual 20) and cutadapt (v1. 16)  (58). For the alternative splicing analysis, the raw reads were annotated on GRCh37. 75 EnsEMBL reference annotation by Tophat2 (v2. 0. 13) and analyzed using only reads on exonics junctions with FaRLine pipeline and FasterDB database  (59). Exons were considered differentially spliced when their adjusted P-value was <0. 05 and their DeltaPSI value was >0. 1. Data are available on GEO database (GSE161897).
Acknowledgements I-Stem  is part of the  Biotherapies Institute for Rare Diseases (BIRD)  supported by the  Association Française contre les Myopathies (AFM-Téléthon ). We thank  Geneviève Gourdon 's team for the southern blot analyses of the CTG repeats length. We gratefully acknowledge support from the  PSMN (Pôle Scientifique de Modélisation Numérique)  of the  ENS of Lyon  for computing resource. We thank  Lina El-Kassar  and  Karine Giraud-Triboult  for karyotyping the cell lines.
9 Finally one third of households are headed by women, but this measure refers to various situations of dependency or vulnerability as well as autonomy, notably in the cities, thus not exclusively a measure of heads of poor households. On a regular basis, large national surveys progressively follow one after the other, even more with the launch of national plans to eradicate poverty. 10 hey provide quantitative data that records and follows the evolutions, allowing us to reconstruct historical trends, to classify the chronic nature of poverty, to identify populations below the poverty line, and to assess the persistence of extreme poverty and the levels of prevalence of hunger. General trends come out from these datasets. Beginning in the 1990s, but starting earlier in the 1980s, a general deterioration of key indications is visible (poverty levels, hunger, demographic indicators) with regional and cyclical patterns revealing the impact of droughts, prices and sociopolitical conflicts.
416 in 2018 by the Gini index. This measure, albeit high, is well below that of other southern and central African countries 12 and tends to dip in the countryside, but remains high in the cities where the wealth is concentrated. In 2016 the first quintile of the population (e. g. the richest 20%) had access to 56% of income whilst the bottom quintile (e. g. the poorest 20%) had only 4%, and in the cities the first two quintiles had access to 90% of income (data from KBS Basic Report on Well-being in Kenya). Another measure of inequality is derived by examining paid employment or self-employment-be it formal or informal work-and wage conditions, which both reveal structural constraints and positive development, even with distortions. Due to the population growth and the inertia of these trends, the number of employees, a measure smaller than the total working population, doubles every 6 to 7 years:  1.
Acknowledgement For their welcome and the exchanges that made me discover a vibrant universe of creativity, all my gratitude goes to  Alan Donovan ,  Peter Elungat ,  Hadija Ernst ,  Alan Githuka ,  Otieno Gomba ,  Johannes Hossfeld ,  Danda Jaroljnek ,  Cartoon Joseph ,  Sebastian Kiarie ,  Richard Kimathi ,  Peterson Kamwathi ,  Ivan Korsak ,  Otieno Kota ,  Carol Lees ,  Dominic Martin ,  James Mbuthia ,  Chain Muhandi ,  Patrick Mukabi ,  James Muriuki ,  Jesse Nganga ,  Judy Ogana ,  Thom Ogonga ,  Paul Onditi ,  Samantha Ripa di Meana ,  Rahab Shine ,  Miriam Syowia Kiambu ,  Michael Soi ,  Shine Tani ,  Chelenge van Rampelbergh ,  Mark van Rampelbergh ,  Xavier Verhoest ,  Sane Wadu ,  Margaretta  (Swigert) wa Gacheru,  Yoni Waite ,  Harsita Waters  and  Frank Whalley. A spare of thought for  Deissy Rodriguez-Torrès  who introduced me to Nairobi in 1998 as part of her project " Contemporary Nairobi.
The Real-Time Working Group (RTWG) of the International GNSS Service (IGS) is dedicated to providing high-quality data and high-accuracy products for Global Navigation Satellite System (GNSS) positioning, navigation, timing and Earth observations. As one part of real-time products, the IGS combined Real-Time Global Ionosphere Map (RT-GIM) has been generated by the real-time weighting of the RT-GIMs from IGS real-time ionosphere centers including the Chinese Academy of Sciences (CAS), Centre National d'Etudes Spatiales (CNES), Universitat Politècnica de Catalunya (UPC) and Wuhan University (WHU). The performance of global vertical total electron content (VTEC) representation in all of the RT-GIMs has been assessed by VTEC from Jason-3 altimeter for 3 months over oceans and dSTEC-GPS technique with 2 d observations over Published by Copernicus Publications.
The estimated electron density is condensed at a fixed effective height (450 km) for the generation of a single-layer VTEC map, and then the VTEC interpolation method is adopted in a sun-fixed geomagnetic reference frame for filling the data gap on a global scale. From 2011 to 2019, the kriging technique is selected by UPC for real-time VTEC interpolation. And the spherical harmonic model has been adopted by UPC since 8 September 2019. Recently, a new interpolation technique, denoted atomic decomposition interpolator of GIMs (ADIGIM), was developed. Since the global ionospheric electron content mainly depends on the diurnal, seasonal and solar variation, ADIGIM is computed by the weighted combination of good-quality historical GIMs (e. g. , UQRG) with similar ionosphere conditions. The database of historical GIMs covers the last two solar cycles since 1998.
It is assumed that VTEC I,t can be approximated by D g,I,t and α t , while D g,I,t is the VTEC extracted at IPP from historical databases of GIM g (for UPC, the UQRG is used), and α t is the unknown weight vector of each historical GIM at epoch t. αt is the estimated weight vector of each selected UQRG at epoch t. The estimated weight vector αt is obtained by the LASSO regression method with loss function norm 2 and regularization norm 1. 2 is the norm for minimizing the Euclidean distance between observed VTEC measurements and historical UQRG databases at epoch t. 1 is the regularization norm for penalizing the approximation coefficients to limit the number of UQRG involved in the estimation, and ρ controls the sparsity of solution. G t is the generated UPC RT-GIM of epoch t and is the weighted combination of historical UQRG.
For mathematical convenience, each 2-D GIM is reformed as a 1-D vector (i. e. , the columns are stacked along the meridian in order to create a vector of all the grid points of the map). This is justified because the measure of similarity is done over cells of 2. 5 • ×5. 0 • in the maps, and therefore the underlying R 2 (coordinate space of dimension 2) structure is not relevant for computing Euclidean distances in 2 norm. D t is the selected historical UQRG database with similar ionosphere conditions at epoch t.
Wuhan University The daily rapid and final GIM products have been generated with new WHU software named GNSS Ionosphere Monitoring and Analysis Software (GIMAS) since 21 June 2018  (Zhang and Zhao, 2018). At the end of the year 2020, WHU also published a first RT-GIM product. WHU uses the spherical harmonic expansion model, and the formula is identical to Eq. (4). Currently, only the GPS real-time data streams from about 120 globally distributed IGS stations are used. The double-frequency code and carrier phase observations with a cut-off angle of 10 • are used to gather precise geometry-free ionospheric data with the CCL method as Eq. (  3 ) and ionospheric mapping function with the layer height of 450 km. In order to avoid the influence of satellite and receiver DCB on ionospheric parameter estimation, WHU directly uses the previous estimated DCB from the WHU rapid GIM product.
The performance of IGS RT-GIMs In this section, the performance of IGS RT-GIMs was analyzed and compared with rapid IGS GIMs as well as IGS combined final GIM. It should be noted that the RT-GIMs were gathered with BKG Ntrip Client (BNC) software  (Weber et al. , 2016)  and generated by received spherical harmonic coefficients from different centers as in Table  2. And there were two kinds of temporal resolution for received RT-GIMs: the common temporal resolution of 20 min and the full (original) temporal resolution. Since the IRTG is combined every 20 min, we will focus on such a common time resolution to compare the performance. The detail of compared RT-GIMs can be seen in Table  3. The influence of temporal resolution on RT-GIMs was also shown in this section. Before detailing the Jason-3 VTEC and GPS-dSTEC assessment, it should be taken into account that the GIM error versus Jason VTEC measurements have a high correlation with the GIM error versus dSTEC-GPS measurements, although the Jason VTEC measurements are vertical and the dSTEC-GPS measurements are slanted.
As demonstrated in Hernández-Pajares et al. (  2017 ), the Jason-3 VTEC assessment and dSTEC-GPS assessment are independent and consistent for GIM evaluation. In other words, the slant ray path geometry changes do not affect the capability of dSTEC reference data to rank the GIM, and the electron content between the Jason-3 altimeter and the GNSS satellites does not significantly affect the assessment of GIMs based on Jason-3 VTEC data.
Data availability The IGS real-time combined GIMs during the testing period are available from Zenodo at https://doi. org/10. 5281/zenodo. 5042622 (Liu et al. , 2021b)  in IONEX format  (Schaer et al. , 1998). In addition, more archived IGS combined RT-GIMs can be found at http://chapman. upc. es/irtg/archive/ (Liu and Hernández-Pajares, 2021a) , and the latest IGS combined RT-GIMs are available in real-time mode at http://chapman. upc. es/irtg/last_results/ (Liu and Hernández-Pajares, 2021b).
6 E ). Interestingly, LN exit of Th17 cells but not Th1 cells was impacted by the abrogation of autophagy in LECs, suggesting assessed by histology analysis of knee sections at day 50 (six or seven mice/group). Representative images are provided, and arrowheads indicate inflammatory areas. Histograms represent global inflammation scores (sum of two knees per mouse). (C) mSAA and IL-6 mRNA levels in dLNs and paws at day 31 of CIA (four to six mice/group). (D) CIA was induced in Tx-treated Atg5 WT and Atg5 ΔFlt4 mice. Clinical scores (paw thickness) were assessed at indicated time points. Data are representative of two independent experiments with six to eight mice/group. (E) CIA was induced in Tx-treated Atg5 WT and Atg5 ΔProx1 mice. Flow cytometry analysis of indicated T cell subsets infiltrating hind-joint legs at day 31 (five or six mice/group).
Two different enzymes, SphK1 and SphK2, respectively, are implicated in the generation of S1P. Analysis of amino acid sequences of SphK1 and SphK2 using the iLIR database software revealed that both enzymes exhibited LC3 interacting motifs. However, only SphK1 LIR motifs displayed a PSSM score >12, predicting an efficient targeting for SphK1, but not for SphK2, toward autophagosomes (Fig. S5 A ). In vitro starvation of LC3-GFP LECs further showed that autophagosomes (LC3-GFP + ) colocalized with SphK1 but not with SphK2 (Fig. 9  E and Fig. S5 B ). Western blot analysis revealed that following starvation, Atg5 WT LECs exhibited higher levels of LC3-II, validating the induction of autophagosome formation (Fig. 9 F ). Interestingly, this observation was associated with decreased SphK1 protein level in Atg5 WT LECs (Fig.
Accordingly, starvation of Atg5 ΔProx1 LECs did not compromise T cell transmigration (Fig. 9 G ). We further validated these results using an inflammatory stimulus instead of starvation. LECs isolated from LC3-GFP mice treated with IFN-γ independent experiments with four or five mice for each time point. One-way ANOVA; * P < 0. 05 and *** P < 0. 001. Error bars correspond to lower and higher values for each group. (B) LC3-GFP mice were injected s. c. with IFN-γ and CQ. LECs were sorted from dLNs, and colocalization of autophagosomes (LC3-GFP + organelles) and MHCII compartment was examined by microscopy. (C) Pattern of indicated PTA mRNA expressed by LECs, BECs, and FRCs sorted from steadystate LNs (pool of three or four mice) and PSSM scores of their amino acid sequences determining their potential targeting toward autophagosomes (iLIR database software).
(F) SphK1 protein levels and LC3-II/LC3-I ratios (fold change) on sorted LECs from Tx-treated Atg5 WT and Atg5 ΔProx1 mice, cultured and starved or not for 4 h. Data are representative of three independent experiments with two or three mice/group. (G) LECs sorted from Tx-treated Atg5 WT and Atg5 ΔProx1 mice were cultured in the bottom part of a transwell membrane and starved or not for 16 h. Activated CD4 + T cells, treated or not treated with FTY-720, were added in the upper part. After 4 h, CD4 + T cell transmigration was analyzed by flow cytometry in the bottom part. Results are expressed as the ratio of migrated CD4 + T cells normalized to the control group (nonstarved WT LECs without FTY-720). Data are representative of three independent experiments with three or four mice/group. (H) S1P quantification (ELISA) from sorted Tx-treated Atg5 WT and Atg5 ΔProx1 LECs cultured in RPMI with 1% of BSA (FBS free) for 48 h (two independent experiments with five or six mice/group).
After washing, secondary antibodies against chicken Alexa Fluor 488 for GFP staining and antirabbit Alexa Fluor 546 (1/1,000e; Thermo Fisher Scientific) were used for 2 h at RT (in the dark). Samples were washed and stained for 5 min with DAPI. Pictures were acquired using a confocal microscope (LSM700; Zeiss). Distances between LECs (Lyve-1 + cells) and CD4 + OT-II Th17 cells (RORγt-GFP + cells) were blinded and calculated using ImageJ software. Cell isolation dLNs were cut into small pieces and digested in RPMI containing 1 mg/ml collagenase IV (Worthington Biochemical Corporation), 40 µg/ml DNase I (Roche), and 2% FBS for 30 min at 37°C. Remaining tissue pieces were further digested with 1 mg/ml collagenase D and 40 µg/ml DNase I (Roche) and 1% of FBS for 20 min at 37°C. The reaction was stopped by adding 5 mM EDTA and 10% BSA.
In vitro suppression assay 2 wk after Tx treatment, mice were irradiated twice a day (500 mGy). The day after irradiation, 5 × 10 6 BM cells from Foxp3 RFP RORγt GFP mice were injected (i. v. ), and the mice received antibiotics in water for the next 2 wk. CIA was induced in BM chimeric mice after 8 wk, and T reg cells from dLNs were sorted (based on RFP expression) after 26 d with Aria sorter (BD Bioscience). T reg cells were co-cultured at different ratios with purified CTV-labeled naive CD25 neg CD4 + T cells (magnetic beads isolation kit; Miltenyi Biotec) stimulated with anti-CD3 antibody (0. 25 µg/ml; eBioscience), and BM-derived DCs were differentiated during 9 d with GM-CSF as described previously  (Lippens et al. , 2018). 3 d after, naive T cell proliferation was assessed by flow cytometry, and the proliferation index was calculated using FlowJo software.
LIR database analysis For each protein, amino acid sequences were analyzed using a published iLIR database  (Nezis, 2021)  to obtain predictive LIRs and their PSSM scores. Predictive LIRs with PSSM scores >12 give reliable prediction for targeting protein toward autophagosomes (with an accuracy >75. 4% and sensitivity >88. 9%; Kalvari et al. , 2014).
The fluorescence was detected with an electron-multiplying charge-coupled device camera (Evolve 512 10 MHz Back Illuminated; Photometrics) and a 10×/0. 3 numerical aperture water immersion objective (W Plan Apochromat; Zeiss) using three lasers with the excitation wavelengths of 405 nm, 488 nm, and 640 nm (La-serStack v4 Base, 3i) and appropriate band-pass-emission filters (Semrock). Three-dimensional image stacks were obtained by sequential acquisition of multiple fields of views along the z axis using a motorized XY-stage (ProScan; Prior). SlideBook software (6. 0. 17, 3i) was used for image acquisition, and the subsequent deconvolution, creation of maximum projection, and generation of montage images from contiguous positions were performed using the Fiji plugins Deconvolutionlab2 and grid/collection stitching  (Sage et al.
Acknowledgments The authors thank  J. P. Aubry-Lachainaye ,  C. Gameiro , and  G. Schneiter  for excellent assistance in flow cytometry. We also thank  T. Petrova  for providing the iLECs,  C. Gabay ,  C. Halin , and  C. Münz  for valuable discussions,  B. Kwak  for help with Western blot experiments,  P. Castets  for help with p62 staining, and  L. Garnier  for critical reading of the manuscript. We are grateful to  N. Mizushima  and  O. Sagrario  for providing LC3-GFP and Flt4Cre ERT2 mice, respectively. This work was supported by  Carigest SA  and the  Swiss National Science Foundation  (grants  310030_166541  and  310030_185255  to  S. Hugues ).
Data analysis of histology Counts of premotor neurons and Lmx1b neurons. Cells expressing mCherry and/or nlsLacZ were counted in a spheroid of fixed dimension and position delimitating the ipsilateral dorsal IRt, drawn on the approximately seven alternate sections that were in register with the compact formation of MoA; n = 4 animals, 87 ± 20 SEM premotor neurons per animal. Cells expressing Phox2b and/or Lmx1b were counted as above from one side; n = 3 animals, 1321 ± 46 SEM neurons per animal. Inputs to IRt Phox2b. Labeled neurons were manually annotated as IRt seed neurons (GFP + mCherry+) or monosynaptic input neurons (mCherry+) in ImageJ. The annotated sections were aligned to the Allen Brain Atlas using QuickNII (https:// www. nitrc. org/projects/quicknii) transforming the annotations into Allen Brain Atlas coordinates and corresponding Allen Brain Atlas brain structures were identified using CellfHelp https://doi.
37 NA) and a zirconia mating sleeve (Thorlabs). Laser output was controlled using a pulse generator (accupulser, WPI), which delivered single continuous light pulses of 50-1000 ms or trains of 100 ms pulses at 4 Hz (33% duty cycle), 6 Hz (50% duty cycle), and 7 Hz (67% duty cycle). Light output through the optical fibers was adjusted to ~5 mW at the fiber tip using a digital power meter (PM100USB, Thorlabs). All light stimuli were separated by minimal periods of 10 s. Laser output was digitized at 1 kHz by a NI USB-6008 card (National Instruments) and acquired using a custom-written software package (Elphy by G Saddoc, https://www. unic. cnrs. fr/software. html). Photometry. For photometry experiments, a single site fiber photometry system (Doric Lenses Inc, Canada) was used to measure the excited isosbestic (405 nm) and calcium-dependent fluorescence of jGCaMP7s (465 nm).
Doric neuroscience studio software system (Doric Lenses Inc, Canada) was used to operate the photometry hardware and acquire the photometry signal. Briefly, using the "lock in mode" function, and 405 nm LEDs were sinusoidally modulated at 208. 616 and 572. 205 Hz, respectfully (to avoid any electrical system harmonics at 50/60, 100/ 120, and 200/240 Hz) at an intensity of 30 μW and coupled to a patch cable (diam. 200 μm, 0. 57 nA) after passing through an optical assembly (iLFMC4, Doric Lenses Inc, Canada). The modulated excitation signal was then directed through an implanted fiber-optic cannula (diam. 200 μm, 0. 57 NA) onto the IRt via the mated patch cable and the emitted signal was then returned via the same patch cable to a fluorescence detector head, mounted on the optical assembly and amplified.