EMBO/sd-character-level-ner huggingface dataset:
Figure 4A Heatmap of unsupervised hierarchical clustering performed on ER+ BC TCGA based on expression of most matrisome collagens and proteoglycans. Tumor identities ILC (blue) and non-ILC (red) are shown. B Density plot showing the estimated score distributions of ILC and non-ILC tumors based on the expression of matrisome ECM-related genes. The vertical lines identify the medians. Statistical test performed by unpaired Student's t test, two-tailed. C Heatmap of normalized expression levels of LOX family members and ELN in invasive BCs, in ILC (blue) and non-ILC (red) tumors sorted based on CDH1 expression levels. Right, boxplots showing normalized transcript expression levels. The line in the middle of the box is the median. The edges of the box reflect the 25th and 75th percentiles, vertical lines outside the box end at minimum and maximum values. Outliers are depicted as grey dots. Statistical analysis was by ANOVA analysis of the linear model with tumor subtypes and tumor purity as covariates. Adjusted p-values computed by post-hoc tests. Sample size for NSTs n=490 and ILCs n=127. **** p < 0.0001. D Representative RNAscope image of sections from patient ILCs (n=5) stained with anti-LOXL1 probes (red) and counterstained with DAPI (blue). Scale bars; 50 μm. E Representative immunofluorescence image of primary ILC (n=3) stained with anti-LOXL1 (green) and anti-ER (red) antibodies counterstained with DAPI (blue). Scale bars; 50 μm and right inset 30 μm.
Figure 1Human placental syncytiotrophoblast cells express markers of cellular senescence, p16 Sections of normal human post-partum, third trimester, placenta were evaluated by immunofluorescence co-staining for senescence regulators (A) p16 Green label: the syncytiotrophoblast marker βHCG, red label: p16 Blue label: DAPI nuclear stain. Arrowheads indicate positively stained syncytiotrophoblast cells βHCG+/p16+ (A) Scale bar, 50 µm. Human placental syncytiotrophoblast cells express markers of cellular senescence, p21. Sections of normal human post-partum, third trimester, placenta were evaluated by immunofluorescence co-staining for senescence regulators (B) p21. Green label: the syncytiotrophoblast marker βHCG, red label: p21. Blue label: DAPI nuclear stain. Arrowheads indicate positively stained syncytiotrophoblast cells , βHCG+/p21+ (B). Scale bar, 50 µm. (C-F) Sections of human normal third-trimester placentas post-partum (n=4 normal placentas) and IUGR-complicated placentas of the same gestational age (n=4 IUGR placentas) were stained for senescence-related markers of p15 (C), p16 (D), p21 (E), and p53 (F) in the syncytiotrophoblast (n=3 sections, derived from each normal and IUGR placenta). Percentages of positively stained syncytia were quantified (n= at least 12 fields of view from all sections). Scale bar, 100 µm. Arrowheads indicate syncytiotrophoblast cells. Data information: Values are means + SEM of at least three experimental repeats. Statistical significance was determined by unpaired two-tailed Student's t-test (*) p < 0.05; (**) p < 0.01; (***) p < 0.001. (G) Immunoblot analysis of the protein content of p16, p21, p53 and DCR in normal (n=4 placentas) and in IUGR-complicated placentas (n=4 placentas). Each lane represents one independent placenta. (H) Quantitative RT-PCR analysis of p16, p21 and DCR2 expression in IUGR-complicated and in normal placentas. Results were obtained from four human normal and four IUGR placentas. Data information: Values are means + SEM of at least three experimental repeats. Statistical significance was determined by unpaired two-tailed Student's t-test (*) p < 0.05; (**) p < 0.01; (***) p < 0.001.
Figure 4RNA sequencing (RNA-seq) of week 15 COs and transcriptome analysis (WT: n=2, KO: n=4).   Heatmap of 100 upregulated genes (left panel) and 100 downregulated genes (right panel) selected by highest fold change.   RNA sequencing (RNA-seq) of week 15 COs and transcriptome analysis (WT: n=2, KO: n=4). Gene-set enrichment analysis (GSEA) revealed enrichment of genes related to regionalization of the organoids, and decreased expression of genes related to negative regulation of the cell cycle. RNA sequencing (RNA-seq) of week 15 COs and transcriptome analysis (WT: n=2, KO: n=4). Heatmap of Wnt-pathway related genes in 15-weeks COs. RNA sequencing (RNA-seq) of week 15 COs and transcriptome analysis (WT: n=2, KO: n=4). qPCR analysis for selected Wnt target genes validating the results of the RNA- seq. Y-axis indicates relative expression fold change. Data are represented as mean ± SEM. Statistical significance was determined using one-way ANOVA with Tukey's multiple comparisons test (WT: n=4 from 1 batch, KO: n=4 from 1 batch, W-AAV: n=4 from 1 batch). Data information: *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001. Week 16 COs were sub-fractionated into a cytoplasmic (C) and nuclear (N) fractions. The experiment was run twice with a total of 2 WT organoids and 4 KOs organoids (2 for each KO line). KAP-1 marks the nucleus and HSP90 marks the cytoplasm. The numbers at the bottom are a quantification of the nuclear fraction of β-catenin band intensities normalized to the cytosolic fraction [β-C (N/C)]. Heatmap showing the expression levels of markers of the six different layers of the human cortex in week 15 organoids from deepest to the most superficial: TBR1, BCL11B (CTIP2), SATB2, POU3F2 (BRN2), CUX1, RELN. IF staining in week 15 COs validating the decreased levels of the deep-layer cortical markers CTIP2 (BCL11B) and TBR1, and superficial-layer marker SATB2 (WT: n=3, KO: n=4, W-AAV: n=4). Scale = 50µm.   Quantification of the cortical markers seen in G, normalized to the total number of nuclei. Y-axis indicates the fold change compared to the average of the WT COs. The boxplot represents the 1st and 3rd quartile, with its whiskers showing the minimum and maximum points and a central band representing the median. Statistical significance was determined using one-way ANOVA with Tukey's multiple comparisons test (WT: n=9 from 3 batches, KO: n=16 from 3 batches, W-AAV: n=4 organoids from 1 batch).   Data information: *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001.
– Tau protein is not involved in regulating the rate of adult hippocampal neurogenesis under basal conditions.Figure 1A-B Representative image of a proliferative cell in the DG labeled with an anti-PH3 antibody (green) (A) and quantification of the number of PH3+ cells in the DG of WT and Tau-/- mice (B) (mean ± SEM; n= 10 mice WT, n= 8 mice Tau-/-; Student´s t-test). C-D Representative image of an apoptotic cell in the DG labeled with an anti-fractin antibody (red) (C) and quantification of the number of fractin+ cells in the DG of WT and Tau-/- mice (D) (mean ± SEM; n= 10 mice WT, n= 8 mice Tau-/-; Student´s t-test). E-F Schematic diagram of the cell survival experimental design using thymidine analogs (F) and quantification of the percentage of surviving cells in Tau-/- mice as compared to WT mice at each cell age (1-, 2-, 4-, 6- and 8-week-old cells) (F) (mean ± SEM (normalized data); Student´s t-test). G Schematic diagram of the cell markers representative of each maturational stage during adult hippocampal neurogenesis. H Quantification of the percentage of 1-, 4- and 8-week-old newborn neurons that express the DCX neuroblast marker and the NeuN mature neuron marker in WT and Tau-/- mice (χ2 test). I-J Representative images of progenitor cells in the DG labeled with anti-Sox2 (red) and anti-BLBP (green) antibodies (I), and neuroblasts and immature neurons labeled with anti-DCX (red) and anti-calretinin (green) antibodies, respectively (J).K-N Quantification of the number of Sox2+ (K), BLBP+ (L), DCX+ (M) and calretinin+ (N) cells in the DG of WT and Tau-/- mice (mean ± SEM; n= 10 mice WT, n= 8 mice Tau-/-; Student´s t-test).
Figure 4(A) Concept of experiments shown in B-D. (B) Timeline of experiment performed in C, D. (C) Representative IF-FISH images of mitotic spreads in non-treated cell (NT) and following a CENP-AOFF/ON cycle (IAA WO). Chromosomes are contoured by a green (X), magenta (Y) or white (other autosomes) dashed line. The centromeres of chromosome X/Y are highlighted by a green/magenta arrow. Scale bar, 2 µm. (D) Quantification of CENP-C (as read-out of CENP-A) presence at the X (green) or Y (magenta) centromere in the indicated cell lines. Each dot represents one experiment. Error bars represent SD from 3 independent experiments. Unpaired t test, **p=0.0042. (E) Schematic illustration of CRISPR/Cas9-mediated genome editing of the non-essential RPS4Y gene on the Y chromosome with the insertion of a neomycin resistance cassette. (F) Experimental set-up for G, H. (G) Representative IF-FISH images showing CENP-C localization on the Y chromosome in cell growing under selective pressure (G418) following a CENP-AOFF/ON cycle. Chromosomes are highlighted by a white dashed contour line. CENP-C was found at the native centromere position (top panel, blue), the Y chromosome fused to another chromosome indicated by the increased size of the chromosome and the absence of Chr-Y painting probe staining (second panel, orange) or CENP-C was found on a different location on the Y chromosome and did not overlap with Cen-Y DNA (lower panels, red). Scale bar, 2 µm. (H) Quantification of indicated events depicted in G. Each dot represents one experiment (>20 spreads for experiment). Error bars represent SEM from 3 independent experiments. Unpaired t-test, *p=0.0137 and 0.039.
– Schematic model.Figure 9A Under basal conditions, Tau protein is involved in the maturation of newborn granule neurons in the DG. In the absence of Tau, newborn neuron dendritic arborization is transiently altered and PSD formation is impaired (decreased PSD density and area were found in the distal dendrites).B Acute stress decreased the survival of immature 1-week-old newborn granule neurons, an effect that is less pronounced in Tau-/- animals as compared to WT. Furthermore, acute stress also impairs dendritic branching and reduces PSD density and MFT area in 8-week-old fully mature newborn neurons of WT animals. In contrast, these effects are not observed in Tau-/- mice.C EE increases 8-week-old mature newborn neuron survival, dendritic branching, MFT area and PSD density in the proximal dendrites, and decreases PSD area in the distal dendrites of WT neurons. However, these effects are less pronounced or even inexistent in the absence of Tau. Actually, EE further reduces the density and area of the PSDs in Tau-/- distal dendrites.
An animal model recapitulating most of the histological hallmarks of PH secondary to PF.Figure 4(A) Masson's trichrome representative images of lung fibrosis and quantification two weeks after PBS or bleomycin instillation. Quantification of (B) fibronectin, (C) Collagen I and (D) Collagen III mRNA. (E) Schematic of experimental protocol. Animals were divided into 4 groups: control (Ctrl), pulmonary fibrosis (PF), pulmonary hypertension (PH) and PF secondary to PH (PF-PH). At day 0, rats in PF and PF-PH groups received an intra-tracheal instillation of Bleomycin (2.5mg/Kg), whereas Ctrl and PH groups received a PBS instillation. At day 14, PH and PF-PH groups received a subcutaneous injection of monocrotaline (MCT, 60mg/kg), whereas Ctrl and PF groups received a subcutaneous injection of PBS. (F) Right ventricular systolic pressure (RVSP) and (G) Right ventricular hypertrophy index following the experimental protocol. (H) Masson's trichrome representative images and quantification of Ashcroft score in the experimental model. Relative expression of fibronectin (I), collagen I (J) and collagen III (K) mRNA normalized to GAPDH. (L) Masson's trichrome representative images and quantification of vascular remodeling. (M) Masson's trichrome representative images and quantification of the vascular remodeling between fibrotic and non-fibrotic areas in the experimental model. The number of samples per group for each experiment are included within each bar graph.
Figure 5A Fold-change of each annotated mRNA (log2FC, relative to the EV control), plotted against its q-value (-log10). mRNAs showing significant up- and down-regulation (qval<0.05) are marked in red and blue, respectively. The values reported in the graphs indicate the total numbers of up- and down-regulated genes (qval<0.05) and of the subset regulated above a defined threshold of |log2FC|>0.5. B Heatmaps representing the same log2FC values as in A (restricted to those mRNAs with qval<0.05 in at least one of the MycER samples). The two heatmaps differ in the samples driving the clustering, indicated by the asterisks at the top. C-E Scatter plots confronting fold-change values (defined as in A) in response to MycERWT (x-axis) and MycERHEA (y-axis), showing the following groups of mRNAs: (C) all of the mRNAs called as DEGs (qval<0.05) in at least one of the samples; (D) MycERWT-regulated DEGs (whether regulated or not by MycERHEA); (E) MycERHEA-specific DEGs (excluding those regulated by MycERWT). F Percentage of promoters with the indicated DNA motifs under the ChIP-seq peak (±100 bp from the peak summit) within each regulatory class (no DEG, UP or DOWN) for either MycERWT (left) or MycERHEA (right). p-values calculated with Fisher's exact test. G Percentage of promoter-associated ChIP-seq peaks with the indicated motifs, as a function of peak intensity (binned in deciles: 1-10) for either MycERWT (top) or MycERHEA (bottom). H Percentage of DEG UP genes (qval<0.05) as a function of peak intensity (binned as in G). Statistical test: Chi-squared against the "no motif" condition, performed on the entire series.
Most abundant miRNAs in mammalian oocytes.Figure 1(A) miRNA abundance in RNA-sequencing samples from murine, porcine, and bovine oocytes Each graph shows on the y-axis reads per million of 19-32 nt reads for miRNAs and on the x-axis miRNAs ordered by name. (B) Schematic depiction of miRNA precursors. Precursor sequences and predicted basepairing were adopted from miRbase miRNA annotations miR-10b secondary structures in the mirRbase contained two different basepairing versions in the loop, the alternative folding is displayed (C) qPCR quantification of ssc-miR-205 and bta-miR-10b miRNAs in murine (M.m.), porcine (S.s.), and bovine (B.t.) oocytes, respectively. Shown are a mean values from three independent experiments. Error bars = SD. Detailed information concerning miRNA quantification is provided in the Methods section.
Nanog deletion triggers gastric differentiation in KL model.Figure 2(A, Human (A) lung sections were stained with H&E or with Periodic Acid Schiff (PAS) and Alcian blue (AB). Scale bar, 50 μm. B) KLN murine lung sections were stained with H&E or with Periodic Acid Schiff (PAS) and Alcian blue (AB). Scale bar, 50 μm. (C) Statistical analysis of mucinous tumor numbers (no.) in KL (n = 7) or KLN (n = 7) mice. Significance was calculated by two-tailed unpaired Student's t-test with Welch's correction. Results were shown as mean. **p=0.0066. (D) Representative pictures of lung tumors at 4 weeks and 8 weeks post Ad-Cre infection in KLN mice. Scale bar, 50 μm. (E) Statistical analysis of IMA ratio at 4 weeks and 8 weeks post Ad-Cre treatment (n=5 per group). Results were shown as mean ± SEM. (F) Statistical analysis of ratio of mucinous phenotype in AAH, AD, and ADC (n=5 per group). Results were shown as mean ± SEM. Significance was calculated by one-way ANOVA with Dunnett's multiple comparisons test. *p=0.0215. (G) qPCR analysis of stomach-restricted gene set between KL ADC and KLN mucinous tumor sections (n=3 or 4 per group). Results were shown in a box and whisker plot with the minimum value, first quartile, median, third quartile and maximum value. The box represented the 50% of the central data, with a line inside represented the median. The significance was calculated by two-tailed unpaired Student's t-test with Welch's correction. *p=0.0260 (Hnf4α), *p=0.0275 (Vsig1), *p=0.0122 (Gkn3), *p=0.0324 (Ctse), **p=0.0084 (Onecut2). (H) Representative histological and IHC staining for HNF4α, GKN1, NKX2-1, MUC5AC, CK20 in lung tumors derived from ADC and IMA. Scale bar, 50 μm.
Figure 6A. Schematic representation of MAR (Matrix Attachment Region) within FOXM1 locus. Arrows show the location of PCR primers for ChIP experiments. B. ChIP assays with the SATB2 antibody or IgG using GSCs, NSTCs and NPCs. PCR primers amplified a fragment flanking the MAR of FOXM1 gene locus. Note that abundant SATB2 binds to the MAR of FOXM1 gene locus in GSCs. C. qPCR analysis of ChIP assays with the SATB2 antibody or IgG using GSCs transduced with shNT or shSATB2 (n=3). PCR primers amplified a fragment flanking the MAR of FOXM1 gene locus. Silencing SATB2 decreased its binding amount to the MAR of FOXM1 gene locus. D. CoIP assays of endogenous protein interaction in GSCs. Immunoblots of precipitated proteins or total lysates were performed using indicated antibodies. Note that SATB2 associates with endogenous CBP while not P300. E. qPCR analysis of ChIP assays with the CBP antibody or IgG using GSCs transduced with shNT or shSATB2 (n=3). PCR primers amplified a fragment flanking the MAR of FOXM1 gene locus. Silencing SATB2 reduced the binding of CBP to the MAR of FOXM1 gene locus. F. qPCR analysis of ChIP assays with the indicated antibody (AcH3K18, AcH3K27, AcH4) using T3359 GSCs transduced with shNT or shSATB2 (n=3). PCR primers amplified a fragment flanking the MAR of FOXM1 gene locus. Silencing SATB2 reduced acetylation of H3K18, H3K27 and H4 levels on the MAR of FOXM1 locus. G. qPCR analysis of FOXM1 mRNA expression in T3359 GSCs transduced with shSATB2 or shCBP or both (n=3). H. Immunoblot analysis of FOXM1 expression in T3359 GSCs transduced with shSATB2 or shCBP or both.
Figure 4(A) IL-8 released by human THP-1 macrophages stimulated with purified PLY, LLO or SLO (0.5 μg/ml) in the presence or absence of 100 μM peptides P2, P3 or control peptide CP2 for 18 h. Cholesterol (100 μM) was used as positive control to inhibit hemolysis. Data are mean ± s.e.m from three independent experiments. **** denotes P< 0.0001 by two-way ANOVA with Bonferroni post hoc test for multiple comparisons. n.s. denotes not significant. Exact P values are shown in Appendix Table S4. (B) Schematic showing the cellular architecture of the 3D lung epithelial model. (C) 3D volume images of the GFP-lung epithelial models at 1 h and 3 h post stimulation with 1 μg/ml PLY in the presence or absence of 100 μM peptide P2 or the control peptide CP2. Images are representative of two independent experiments with n=3 models/condition. (D) Invasion of wild-type pneumococci T4 (TIGR4) or its isogenic PLY mutant T4Δply into the lung epithelial models (n=3/condition) in the presence or absence of 100 μM peptide P2 or the control peptide CP2 at 2h post infection was measured using CFU viability assay following gentamicin killing of extracellular bacteria. Anti-PLY was used as control to test the effect of blocking PLY. Data in d and e are mean ± s.e.m. of n=3 models/condition from two independent experiments. % bacterial entry = (bacteria uptaken/input) x100. ** denotes P < 0.01 by one-way ANOVA with Dunnett's post hoc test for multiple comparisons. n.s. denotes not significant. Exact P values are shown in Appendix Table S4. (E) Human DCs were infected with type 4 and type 2 pneumococci, T4 and D39, respectively, at MOI of 10 in the presence or absence of 100 μM peptides, P2 or CP2, and intracellular bacteria were counted at 3 h post infection following gentamicin killing of extracellular bacteria. Cytochalasin D (0.5 mM) was used as negative control to inhibit phagocytosis. Anti-PLY was used as control to test the effect of blocking PLY. Data are mean ± s.e.m. of three independent experiments. **** denotes P < 0.0001 by two-way ANOVA with Bonferroni post hoc test for multiple comparisons. n.s. denotes not significant. Exact P values are shown in Appendix Table S4. (F) DCs were infected with the unencapsulated pneumococcal strain T4R in the presence of 100 μM peptides, P2 or CP2 at MOI of 10 for 2 h. Immunofluorescence microscopy images show that in DCs treated with peptide P2 (but not the control peptide CP2), intracellular T4R (green) do not co-localize with MRC-1 (red), but with the autophagy protein LC3B (cyan). Images are representative of three independent experiments. Scale bars, 10 μm. In magnified images, scale bars, 5 μm. Arrows indicate regions of co-localization of intracellular T4R with MRC-1 and LC3B. (G) Quantification of percentage of intracellular S. pneumoniae (n=50) in infected DCs that co-localize with MRC-1 and LC3B. Data are mean±s.e.m from two independent experiments. **** denotes P <0.0001 by two-way ANOVA with Bonferroni post hoc test for multiple comparisons. n.s. denotes not significant. P values are shown in Appendix Table S4.
Schema of the effect of HTT phosphorylation and TBK1 on aggregation: (A) Effect of S13 and/or S16 phosphorylation on HTTex1 aggregation.Figure 8(A) Effect of S13 and/or S16 phosphorylation on HTTex1 aggregation. HTTex1 forms a tadpole-like monomer structure and N17-driven interaction may further drive HTTex1 oligomerization and fibril formation. Phosphorylation at S13 and S16 destabilizes the helix at N17 that leads to inhibition of the formation of HTTex1 fibrils. (B) Effect of TBK1 on HTT in the cellular HD model. TBK1 and TBK1 Δ690-713 both phosphorylate monomeric or soluble HTTex1 72Q at S13 residue leading the reduction of the aggregation, but TBK1 also reduces the aggregation of both HTTex1 and HTTex1 S13A/S16A through the lowering of the HTT levels at the monomeric stage by enhancing the autophagic degradation. TBK1 Δ690-713 only reduces the aggregation of phosphorylation-competent HTTex1 but does not reduces the aggregation of HTTex1 S13A/S16A highlighting the role of S13 phosphorylation in aggregation inhibition. (C) TBK1 effects on different stages of autophagy. TBK1 is known to phosphorylate autophagy adaptors p62, OPTN that bind ubiquitinated substrates like proteins or damaged mitochondria and recruit LC3 and increase the autophagic clearance of substrates. (D) TBK1 does not phosphorylate HTTex1 in inclusion/ fibrils or promote their clearance/ disaggregation. When HTT was already aggregated in cells or when in fibril form in vitro, possibly S13 residue is not accessible for TBK1 phosphorylation as N17 was shown to be collapsed on fibrillar core or it is near the core. Also, TBK1 mediated autophagy flux was not able to induce the lowering of HTTex1 inclusion. There was no disaggregation of fibrils up on TBK1 kinase in vitro.
+ T cells isolated from patients receiving ART.Figure 5A. EGCG inhibited α-CD3/CD28 reactivation of latent HIV-1. Primary CD4+ T cells were isolated from HIV-1 positive patients on antiretroviral therapy (n=5, P1-P5). Primary CD4+ T cells were treated with α-CD3/CD28 alone or α-CD3/CD28 and 10 µM EGCG. Cell-associated RNA was extracted 7 days post-treatment. The transcription of HIV-1 was determined by real-time qPCR. B. PEBP1 mRNA was induced by EGCG in patient primary CD4+ T cells. Primary CD4+ T cells were treated with 10 μM EGCG. The expression of PEBP1 in the cells was measured by qPCR. C. PEBP1 protein was induced by EGCG in patient primary CD4+ T cells, which was determined by Western blot of whole cell lysate from primary CD4+ T cells. D. EGCG-induced PEBP1 suppressed nuclear entry of NF-κB/p65. This was measured by Western blot of nuclear protein of primary CD4+ T cells treated with α-CD3/CD28 or α-CD3/CD28 plus 10 μM EGCG.