dataesr/scientific-paragraphs-categorization huggingface dataset:
Spectral integration before processing We want our search for drifting bursts to cover a broad range of drift rates, typically 5 ≤| df dt |≤ 25 MHz. s -1. Known drift-rates of Io-Jupiter S-bursts are in the range -15 to -25 MHz. s -1  [10, 34]. The Radon transform performs better far from the horizontal or vertical lines that may be polluted by RFI, i. e. in the range 45 • ± 25 •. At the full resolution of the JunoN receiver, an angle of 45 • corresponds to a drift-rate | δf δt |= 3. 05×10 -3 2. 6×10 -3 = 1. 2 MHz. s -1. A burst drifting at -20 MHz. s -1 makes an angle α at 3. 3 • from the vertical axis in the dynamic spectrum, and thus has all chances of being considered as an RFI. The spectral resolution of JunoN is thus comparatively too high with respect to its time resolution. To correct for that, we pre-integrated the data by a factor 7 in frequency, bringing thus the spectral resolution to 21.
Context observations A further confirmation of the origin of our detected bursts is provided by the overall morphology of the emission around the time of detection of Sbursts of each type (Io-induced, Ganymede-induced and Main aurora). The Main aurora (RH) s 10 MHz. s 1 s 0 MHz. s 1 s MHz. s 1 Fig. 7  Histograms of SNR values for the three types of emissions identified and two polarizations. The same intervals of drift-rate values as in Table  1  are used, and the same color codes as in Figure  3. See text for details. data were recorded by the NewRoutine digital receiver also connected to the NDA. This receiver observes Jupiter for longer periods of time than JunoN (8 hours per day) and provides thus complementary observations with high SNR but lower resolutions than JunoN  [28, 47]. These context dynamic spectra, plotted with a compressed timescale (1-3 hours on Figure  8a-c ), reveal the overall arc-shaped structures in which we detected S-bursts with JunoN.
Acknowledgments. This article is based on observations made with the  Nançay Decameter Array (NDA). The NDA is hosted by the  Nançay Radio Observatory of the Observatoire de Paris  (ORN, supported by  CNRS ,  Université d'Orléans, OSUC, and Région Centre in France). We thank  B. Cecconi  and  E. Thétas  for their help in making the data available, and  F. Jacquet  (the.
Statistical analysis Results obtained from motility and osmolality assessments as well as from fertilization tests were analysed using SPSS 14. 0 (SPSS Inc. , Chicago, USA) and GraphPad Prism 5. 0 for Windows (GraphPad Software, La Jolla, California, USA) statistical software packages. Normal distribution was investigated with Kolmogorov-Smirnov test at the significance level of P < 0. 05. Dataset not showing normal distribution was transformed using arcsine square-root (pMOT, LIN, fertilization and hatching rate) and logarithm (VCL, VSL, ALH, BCF) functions. Experimental and control groups were compared with two-way ANOVA (analysis of variance) followed by Bonferroni's post hoc test or Student's independent t-test (significance level of P < 0. 05).
Experiment 2 Large-scale cryopreservation was experimentally investigated using the sperm obtained from the males reared at the two different temperatures (6 and 12 C). Our results indicated that reduced rearing temperature did not negatively affect the cryopreservation process. This finding is in correspondence with our prior results. Sperm obtained from perch males kept at varying temperatures (6e16 C) was successfully cryopreserved (in 0. 5 mL straw) with (pMOT: 11 ± 7%) or without (pMOT: 18 ± 8%) hormonal stimulation  [23]. To our knowledge, this experiment is the first to report any data on a large-scale freezing method using 5 mL cryotube in Eurasian perch. This methodology caused a clear reduction in most of the measured motility parameters (pMOT, VCL, VSL, ALH). Unstandardized freezing method could lead to decreased sperm movement.
Acknowledgments The study was funded from the  European Union 's  Horizon 2020 research and innovation programme  under grant agreement No. 652831  ( AQUAEXCEL2020 ) from the  TNA  project No. AE090022  (CRYOPERCH). This paper reflects only the authors' view and the  European Union  cannot be held responsible for any use that may be made of the information contained herein. This research was supported by the  Ministry of Innovation and Technology  within the framework of the  Thematic Excellence Programme 2020, National Challenges Subprogramme  ( TKP2020-NKA-16 ). Our experiments were also supported by the  EFOP-3. 6. 3-VEKOP-16-2017-00008project. The project is co-financed by the  European Union  and the  European Social Fund.
3) spectra were collected using 32 scans, 2048 × 256 complex data points, spectral width in F1 5 KHz, in F2 11 KHz, and one-bond J CH = 145 Hz. All J-resolved heteronuclear multiple bond correlation (HMBC) spectra, Bruker pulse program hmbcetgpl3nd, were collected at 800 MHz with the J CH long-range value (cnst13) set to 3-8 Hz. The spectra were processed and assigned, and integration was performed using a Bruker TopSpin 4. 1. 4. Samples were prepared in deuterium oxide (>99. 92%, Apollo Scientific) packed under argon to mitigate interferences arising from paramagnetic oxygen. Conventional NMR nuclei studies (mostly 1 H and 13 C) have been extensively used to provide details around conformational features of heparin/HS ligands. 21 These studies have used natural, semisynthetic and fully synthetic materials with the same overall goal to extract structural information that can be correlated with biological function.
In addition, samples were deparaffinized in xylene at room temperature, coverglasses were used instead of the PAP pen during incubation of primary MUC-2 antibody, and slides were not mounted with Prolong antifade medium. The slides were kept at 4°C until microdissection. Confocal laser scanning microscopy. Images were acquired on a Spinning Disk IXplore using the Olympus cellSens imaging software (V2. 3) at a frame size of 2,048 Â 2,048 with 16-bit depth. A 405-nm laser was used to excite the Hoechst stain (epithelial DNA), 488 nm for Alexa Fluor 488 (mucus), 488 nm for tetramethyl rhodamine isocyanate (actin), and 640 nm for Alexa Fluor 647 (bacteria). Samples were imaged with a 20Â objective or 60Â oil immersion objective. The epithelium-bacteria distance was calculated as follows: animals were randomized and 4 to 5 images showing intact mucus layers were selected from each animal.
This step included five animals from the control group, four from the STR-M group, and nine from the STR-W group. For each image, five representative bacterial cells closest to the epithelium were selected, and the shortest distance was measured to the actin-stained epithelium border using the ImageJ software. Between 20 and 25 measurements were analyzed per animal. Laser capture microdissection. Laser capture microdissection was performed as previously described  (30). Section and microdissection were performed on an Arcturus laser capture microdissection system. Inner mucus layers from the samples were selected, as illustrated in Fig. 6C , and collected on CapSure Macro LCM caps (Arcturus) using a combination of infrared (IR) capture and UV (UV) laser cutting. A mean area of approximately 0.
Then, 20 mL of DNA-free water (Mobio) was added to the column center and the mixture was incubated at room temperature for 10 min, followed by centrifugation at 20,000 Â g for 1 min to collect eluted DNA. DNA isolation, amplification, and 16S rRNA gene amplicon sequencing of fecal and intestinal contents. Fecal and intestinal samples were treated as previously described  (31). 16S rRNA amplicon analysis of fecal and luminal contents. Analysis of the 16S rRNA gene amplicons was carried out essentially as previously described  (31). In brief, sequences were demultiplexed and trimmed to remove barcodes and primers, and sequences below 125 bp or above 180 bp were discarded using the CLC Genomic Workbench (v8. 5) software (CLCbio, Qiagen, Aarhus, Denmark). Using the DADA2 pipeline v1. 12. 44 in the R software (https://www.
R-project. org/), reads were quality filtered (maxEE = 1, maxN = 0, truncQ = 2)and denoised (homopolymer gap penalty = 21, band size = 32), and chimeric sequences were removed. Amplicon sequence variants (ASVs) were assigned taxonomy using the RDP 16S rRNA database (rdp_train_set_18. fa. gz). Using QIIME2 (2019. 1), ASVs with a frequency of ,100 reads across all samples or assigned to Cyanobacteria/chloroplast were discarded. The core diversity metrics function was used with a rarefaction depth of 8,300 reads per sample to create Bray-Curtis distance matrices and alpha diversity measures (Shannon index). Using the rarefy table function, the ASV table was rarefied to 8,300 reads per sample and collapsed to genus levels using the taxa collapse function. Relative abundances at genus level were calculated by total sum scaling normalization.
16S rRNA amplicon sequencing and analysis of inner mucus microbiota. Sequencing of 16S rRNA amplicons from inner mucus samples was performed as previously described using the Illumina MiSeq technology and following the protocol from Earth Microbiome Project  (32). Sequencing reads were demultiplexed and quality filtered using DADA2  (33)  with QIIME2 default parameters. Taxonomy was assigned to the sequences with a 99% threshold of pairwise identity to the Greengenes reference database 13_8. Statistics. Statistics were calculated using GraphPad Prism v. 9. 0. 2 unless otherwise stated. For comparisons of Str r E. coli load, CFU counts were compared using multiple unpaired t tests between groups and paired t tests between days within groups. Alpha diversities were compared using the Wilcoxon matched-pairs signedrank test for same-group comparisons and Kruskal-Wallis test for different group comparisons with adjusted P values (Dunn's multiple-comparison test).
The ANOSIM analyses were based on the Bray-Curtis dissimilarity matrix. All figures were generated using the GraphPad Prism software v 9. 0. 2 (GraphPad Software Inc. , La Jolla, CA). Ethical approval. Ethical approval was given by the Danish Animal Experiments Inspectorate (2015-15-0201-00553). The experiments were overseen by the National Food Institute's inhouse Animal Welfare Committee for animal care and use.
ACKNOWLEDGMENTS We thank  Pi Westi Bondegaard  and  Bodil Madsen  for laboratory assistance,  Asmus K. Olesen  for providing the E. coli K-12 strain, and  Lasse Højlund Eklund Thamdrup  for microcontainer fabrication. We also thank the  IMAG'IC and Genom'IC  facilities at  Cochin Institute, Paris, France , for their contribution during the preparation and confocal visualization of gut histology sections as well as during laser capture microdissection and sequencing. We declare we have no conflicts of interest. The study was funded by the project MIMIO: Microstructures, microbiota and oral delivery, supported by the  Novo Nordisk Foundation  ( NNF17OC0026910 ). B. C. 's laboratory is supported by a starting grant from the  European Research Council (ERC)  under the European Union's  Horizon 2020 Research and Innovation program  (grant agreement  ERC-2018-StG-804135 ), a  Chaire d'Excellence  from  IdEx Université de Paris ,  ANR-18-IDEX-0001 , an  Innovator Award  from the  Kenneth Rainin Foundation , and the national program Microbiote from INSERM.
Study Population Administrative data needed to identify eligible workers and to reconstruct their occupational histories, i. e. , employment periods, workplace locations, were provided by the CEA, Orano, and EDF. It also informed on job title at hiring in the company, which was used to assign a socioeconomic status indicator to each worker: manager or engineer/administrative employee/skilled worker/unskilled worker. If dosimetry records were identified outside the employment periods at the three companies, the date of hire or date of termination was changed accordingly and the worker was considered employed by a subsidiary. As workers may have had multiple employers during the follow-up period, a fixed variable was created to identify the company for which the worker had worked the longest: CEA, Orano, EDF, or other for subsidiaries.
Analyses were also restricted to workers first employed after 1956 because the dosimeters used before 1957 were dosimeters without filters that were likely to overestimate the response at low energies; doses estimated before 1957 are certainly subject to larger measurement errors than those estimated since the dosimeters with filters were used. Coding of medical causes of death is generally suspected to be less accurate at oldest ages: analyses were further restricted to workers aged less than 80 years at the end of the follow-up to investigate the sensitivity of the findings. We report likelihood-based 95% CI for the ERRs. All analyses were performed using the SAS®9. 4 and EPICURE  [34]  software. This study complies with French ethics recommendations on the use of individual health data and has been approved by the French Data Protection Authority (Comité National de l'Informatique et des Libertés, authorization DR-2012-611).
Acknowledgments: IRSN thanks all persons from  CEA, Orano , and EDF who cooperated in the elaboration of the French cohort by providing access to sources of administrative and dosimetric data for this study. The authors thank people from  IRSN 's BASEP unit who helped to extract dose recordings from the SISERI system. Last, the authors also thank  Isabelle Thierry-Chef  and  François Trompier  for their help in the estimation of dose conversion coefficients.
, 2014; Campbell, 2017). The addition of the neprilysin component in LCZ696 augments plasma levels of natriuretic peptides  (Voors et al. , 2013)  that counteract the RAAS and promote vasodilation, natriuresis, and inhibit fibrosis and hypertrophy. Despite recent formal recognition of ARNI by guideline authorities, there is a striking paucity of mechanistic data on the effect of ARNI on cardiac remodeling  (McDonagh et al. , 2021). In this Research Topic, Liu et al. , investigated the mechanisms underlying the cardioprotective action of ARNI in the context of fibrosis and remodeling after AMI that are mostly unknown. They found that the improvement of cardiac function in the ARNI group was more significant than a single RAAS blocker. Then, they investigated the mechanisms involved in the role of the Wnt/β-catenin axis in the prevention of myocardial fibrosis and improvement of myocardial remodeling in the context of ARNI treatment  (Palevski et al.
Indeed, Igh PCR assays detected a slight decrease in D to J H recombination (Figure  S3A ), while V H to DJ H recombination was greatly decreased at V H J558 distal or V H 7183 proximal genes in the absence of the RNA exosome (Figures  S3B to S3D ). To perform an accurate and unbiased quantification of the V(D)J recombination events in these cells, we sorted bone marrow pro-B cells and performed deep RNA-sequencing analysis. We reconstituted the Ig V(D)J sequences from RNA-seq data (using computational tool TRUST4) and performed a V-quest analysis using the international ImMunoGeneTics information system (IMGT) database. These analyses reconstituted the unique V(D)J rearrangements from the RNA-seq data, and we normalized these unique rearrangements to the total number of reads. We were able to reconstitute 7,482 functional V(D)J junctions out of 648,140,008 reads in controls (11.
Bioinformatic analyses RNA exosome subunits expression. -The expression levels of the RNA exosome subunits were extracted from the "ImmGen data browsers microarray" (http:// www. immgen. org), and the values were plotted as heat maps. Motif enrichment (MEME) analysis. -Motif enrichment analysis was performed using MEME Suite 5. 4. 1. Sequence regions 250 base pairs upstream of ATG were retrieved for Dis3 (chr14:99,099,669-99,099,907), Exosc3 (chr4:45,320,580-45,320,829) and Exosc10 (chr4:148,558,216-148,558,471) genes. The following settings were used for motif discovery: Motif discovery mode, classic mode; selected site distribution, any number of repetitions; number of motifs, 3. Data processing. -We use RTA (Illumina) for base calling and bcl2fastq2 (version 2. 17) for converting BCL to fastq format, coupled with adaptor trimming.
The resulting reads were mapped to mm9 genome of house mouse by hisat2 (version 2. 1. 0) (58)  with default parameters. We used StringTie (version 1. 3. 3b; parameter "--rf") (59) for transcript assembly and expression quantification. The read/fragment counts of features were quantified by FeatureCounts and the differential features were detected by DEseq2 with criterion of fold change ≥2 and FDR <0. 05. For visualization in IGV, we merged bam files from replicates by Samtools and generated normalized and strand-specific bedgraph files using Bedtools and properly calculated scaling factors. The bedgraph files were then converted to bigwig by bedGraph2bigWig utility from UCSC. For RNA-seq, we used depth-1x normalization method which normalized the sequencing depth to 1x coverage. For ATAC seq, we use RPM (reads per million mapped reads) normalization.
Differential analysis of lncRNA, eRNA and aTSS-RNA. -lncRNAs that do not overlap with protein-coding exons and with length larger than 200nt were collected. These RNAs were merged across all samples if they overlapped with each other. The merged transcripts were re-quantified using FeatureCounts (parameter "-s 2 -p") to obtain the fragment counts table. DEseq2 was applied to the fragment counts table to obtain the differentially expressed lncRNAs (fold change>=2 and FDR<0. 05). These lncRNAs were shown in the heatmap of FPKM. We collected non-coding RNAs that overlap with enhancer regions as enhancer RNA (eRNA). The enhancer regions were defined by H3K27Ac and H3K4me1 markers from public ChIP-seq (GSM2184223 and GSM2184242). The aTSS-RNA expression was quantified as the non-coding RNA expression in the anti-TSS region (within 2kb upstream of TSS but in the antisense strand).
Supplementary Material Refer to Web version on PubMed Central for supplementary material. (A) Heat map showing RNA exosome subunit expression in mouse B cells, data were obtained from "ImmGen" databank. Relative transcriptomic expression of the RNA exosome subunits is shown in the main B cell populations from various lymphoid organs in adult mice. (B to G) Flow cytometry analysis of Mb1 cre/+ Exosc3 COIN/+, Mb1 cre/+ Exosc10 COIN/+ and Mb1 cre/+ Dis3 COIN/+ B cell populations. Cells were collected form bone marrow, spleen and Peyer's patches and the B cell populations were identified as: (B) pro-B cells (CD43 + , B220 + , CD25 -, IgM -), (C) large pre-B cells (FSC-A high , CD43 low , B220 + , CD25 low ), (D) small pre-B cells (CD43 -, B220 + , CD25 + , IgM -), (E) immature B cells (CD43 -, B220 + , CD25 -, IgM + ), (F) follicular B cells (B220 + CD23 + CD21 dim ), and (G) activated B cells (B220 + , GL7 + ).
Mean is shown, +/-SEM. The V(D)J repertoire was determined by RNA-sequencing of pro-B cells (3 independent experiments), and the number of productive V(D)J rearrangements compared to the total number of reads was used to perform statistical analyses (khi2 proportion test). (G) CDR3 length was analyzed and the violin plots show their distribution in the presence or absence of DIS3 (two-tailed unpaired t-test on combined data from 3 mice). 3C, 3D ) were quantified from these mice. (E) Flow cytometry analysis of Peyer's patches B cell populations from Mb1 cre/+ Dis3 C/+ and Mb1 cre/+ Dis3 C/C mice. (F) Quantification of Peyer's patches resting B cells (B220 + GL7 -). Data were obtained from Mb1 cre/+ Exosc10 C/+ , Mb1 cre/+ Exosc10 C/C , Mb1 cre/+ Dis3 C/+ and Mb1 cre/+ Dis3 C/C mice. (G) Quantification of Peyer's patches activated B cells (B220 + GL7 + ).
Data were obtained from Mb1 cre/+ Exosc10 C/+ , Mb1 cre/+ Exosc10 C/C , Mb1 cre/+ Dis3 C/+ and Mb1 cre/+ Dis3 C/C mice. These results are representative from at least 3 independent experiments, using a total of at least 3 mice per group. Bar graphs show mean value +/-SEM, analyzed with two-tailed unpaired t-test. VJ rearrangements compared to the total number of reads was used to perform statistical analyses (khi2 proportion test). (F) The number of productive Igλ rearrangements among the total number of productive IgL rearrangements was determined (three independent experiments, two-tailed paired t-test). (G) Flow cytometry analyses of Igk expression on B splenocytes (CD19 + ) from V H B1-8 KI/KI Mb1 cre/+ Dis3 C/+ and V H B1-8 KI/KI Mb1 cre/+ Dis3 C/C mice. (H) Quantification of Igk expression on B splenocytes (CD19 + ) from V H B1-8 KI/KI Mb1 cre/+ Dis3 C/+ and V H B1-8 KI/KI Mb1 cre/+ Dis3 C/C mice.
ACKNOWLEDGMENTS We thank  Prof. Michel Nussenzweig  ( Rockefeller University ) for providing V H B1-8 mice,  Prof. Michael Reth  ( University of Freiburg ) for Mb1 cre mice and members of the  Basu laboratory  and numerous colleagues for very important scientific input. We thank the  Columbia University Flow Cytometry Core of the Stem Cell Initiative and Department of Microbiology and Immunology cell sorting facility  (both for FACS and cell sorting) and the  Columbia University Genome Center  (for high throughput genomics).
Fait intéressant, le gène GAST est une cible directe de la voie de signalisation Wnt/ß-caténine/Tcf4  [6]  qui est activée dans de nombreux cancers, et joue un rôle majeur dans la survie des CSCs  [21]. Toutes ces caractéristiques ont amené plusieurs équipes à investiguer la valeur potentielle de hPG 80 dans le diagnostic, l'évaluation du pronostic et le suivi thérapeutique des patients atteints de cancer. [23]. Chez les patients ayant des taux élevés de hPG 80 (> 4,5 pM, n = 63), la survie globale était significativement plus courte que chez les patients ayant des taux plus faibles (n = 33 ; médiane de survie globale : 12 vs 31,2 mois ; p = 0,0031). L'ajout du taux de hPG 80 aux six variables du modèle de risque IMDC (International Metastatic Renal Cell Carcinoma Database Consortium) pourrait contribuer à une meilleure stratification des patients pour le pronostic de survie globale.
(1) New testing units are defined genomewide based on functionally-adjusted Combined Annotation Dependent Depletion (CADD) scores of variants observed in the GnomAD populations, which are referred to as "CADD regions". (2) A regiondependent filtering of rare variants is applied in each CADD region. (3) A functionally-informed burden test is performed with sub-scores computed for each genomic category within each CADD region. Both on simulations and real data, RAVA-FIRST was found to outperform other WGS-based RVAT. Applied to a WGS dataset of venous thromboembolism patients, we identified an intergenic region on chromosome 18 that is enriched for rare variants in early-onset patients and that was that was missed by standard sliding windows procedures. RAVA-FIRST enables new investigations of rare non-coding variants in complex diseases, facilitated by its implementation in the R package Ravages.
Performance of RAVA-FIRST filtering based on adjusted CADD scores To assess the performance of the adjusted CADD scores and the RAVA-FIRST filtering, we evaluated its capacity in discriminating benign from pathogenic variants using the Clinvar database  (29). We computed true positive rate (TPR), true negative rate (TNR) and precision for the RAVA-FIRST filtering and compared the results to the ones obtained by applying a fixed CADD threshold of 10, 15 or 20 on variants annotated with CADD scores v1. 4. After the selection of rare variants included in RVAT (see the Supporting Information), the dataset of analysis contains 70,931 variants of which 25,931 are benign and 45,000 are pathogenic. All filtering strategies show a very high TPR (Fig 1A ), meaning that the majority of pathogenic variants would be selected as qualifying variants for RVAT.