EMBO/sd-character-level-ner huggingface dataset:
Figure 1A, B. Coronal CT image of the chest at baseline with pleural fluid and intralobar septal thickening (arrow) (A), and 3 months after starting trametinib (B). C, D. MR T2 weighted coronal slice of the chest at baseline demonstrating bilateral pleural effusions (arrow heads) and pulmonary interstitial edema (arrows) (C), and 3 months on trametinib therapy (D). IN-DCMRL coronal MIP of the chest at baseline demonstrating dilated and tortuous TD (arrow) with dilated central lymphatic networks and extensive bilateral pulmonary perfusion (arrowheads) (E), and 6 months after trametinib therapy demonstrating dilated and tortuous TD (arrow) with reduction in the extent of the dilated central lymphatic networks and resolution of bilateral pulmonary perfusion IN-DCMRL coronal slice of the chest at the level of the carina demonstrating extensive mediastinal and pulmonary interstitial perfusion (arrows) at baseline (G), and after 6 months of treatment with trametinib (H).
Figure 7(A) HEK293 cells were transfected with ATF3 shRNA or vector (pLKO1), treated with 50 nM MG132, and then subjected to immunoblotting. (B) Individualized XO8 GSCs were transduced with lentiviral shRNAs against ATF3 or control as described in Materials and Methods. After four days, individualized GSCs were treated with 50 nM MG132, and subjected to immunoblotting. (C) XO8 GSCs were transfected with control or CHOP siRNA for 48 hrs and then treated with 50 nM MG132 for 24 hrs. Cell viability was determined using the Trypan blue exclusion assay. Error bars represent the mean ± SD from three independent experiments (*P < 0.05, n=3). For statistical analysis, student t-test (two-sided, one type) were used. (D) Immunoblotting analysis of (C). The cells were collected, lysed, and subjected to immunoblot analysis with indicated antibodies. (E) Wild-type and CHOP-/- MEF cells were treated with MG132 for 24 hrs. Cell viability was determined using trypan blue exclusion assay. Error bars represent the mean ± SD from three separate experiments (*P < 0.05, n=3). For statistical analysis, student t-test (two-sided, one type) were used. (F) Cell lysates obtained in (E) were subjected to immunoblot analysis with anti-PARP-1, anti-CHOP or anti-ATF3 antibody. (G) The expression of NOXA was assessed with real-time PCR using total RNA extracted from XO8 GSCs treated with 50 nM MG132 alone or in combination with each inhibitor of ER stress-driven apoptosis (salubrinal; 15 µM, STK064652; 20 µM, STK047915; 20 µM). The mean +S.D. values from the three independent experiments are shown after normalization to that of control cells treated with DMSO. For statistical analysis, student t-test (two-sided, one type) was used. * P value: salubrinal, 0.0003; STK064650, 0.0036; STK047915, 0.0019. (H) Similar to (G) except that XO8 GSC transduced with lentiviral shRNAs were treated with MG132. The mean +S.D. values from the three independent experiments are shown after normalization to that of control cells treated with DMSO. For statistical analysis, student t-test (two-sided, one type) was used. * P value: #1, 0.026; #5, 0.0033; #6, 0.0482. (I) XO8 GSCs were treated with 20 nM MG132 alone or in combination with each inhibitor as described in (C), and subjected to immunoblotting. Sal.: salubrinal.
A multifactorial adaptive response, rather than initial target inhibition, determines melanoma response to RAF inhibitors.Figure 6Pairwise Spearman's correlation between the 1-h changes in pERK(Thr202/Tyr204) levels as measured by immunofluorescence microscopy and 72-h relative viability both represented by the z-score-scaled AUC of the seven dose-response curves for four RAF inhibitors and one MEK inhibitor across 8/10 cell lines investigated in this study. Comparison of the level of 1-h pERK inhibition for 8 cell lines treated with SB590885 versus PLX4720. Comparison of the 72-h measured relative viability AUC for 8/10 cell lines treated with SB590885 versus PLX4720 Comparison of the level of 1-h pERK inhibition between two cell lines (C32 and WM1552C) treated with four RAF inhibitors and one MEK inhibitor. Comparison of the 72-h measured relative viability AUC between two cell lines (C32 and WM1552C) treated with four RAF inhibitors and one MEK inhibitor. Pairwise Spearman's correlation between the 24-h changes in pS6(Ser235/236) levels as measured by immunofluorescence microscopy and 72-h relative viability both represented by the z-score-scaled AUC of the dose-response curves for four RAF inhibitors and one MEK inhibitor across 8/10 cell lines investigated in this study. Pairwise Spearman's correlation between the 24-h p-cJun levels as measured by immunofluorescence microscopy and 72-h relative viability after treatment with PLX4720 for 8 cell lines. p-cJun levels are averaged over five doses (0.1-5 μM), and viability is represented by the AUC of the dose-response curves. Comparison of the level of 24-h pS6 inhibition for 8 cell lines treated with SB590885 versus PLX4720. Comparison of the level of 24-h pS6 inhibition between two cell lines (C32 and WM1552C) treated with four RAF inhibitors and one MEK inhibitor
LEMD2 and SATB2 regulate neuronal gene transcription in active neurons Primary cortical Bic-treated neurons transfected with either scrambled siRNA (Scrambled) or siRNA against Lemd2 (siLemd2) were subjected to RNA-seq.Figure 4Primary cortical Bic-treated neurons transfected with either scrambled siRNA (Scrambled) or siRNA against Lemd2 (siLemd2) were subjected to RNA-seq. "Volcano plot" of statistical significance against Log2 fold-change between siLemd2- and scrambled siRNA-transfected cultures. The differentially expressed genes are indicated in red (adjusted p-value < 0.05, Log2fold-change > 0.3) and blue (adjusted p-value < 0.05, Log2fold-change < -0.3), n = 3 independent primary cultures. GO enrichment analysis of the differentially expressed genes between siLemd2- and scrambled siRNA-transfected cultures. Rank-rank hypergeometric overlap (RRHO) heatmap comparing the global gene expression signatures of Satb2CamkCre vs floxed cortical cultures (n = 7) and siLemd2 vs scrambled siRNA-transfected cultures (n = 3). For each dataset, all expressed genes (gene counts higher than 10) were ranked by their differential expression p-values and effect size direction. The significance of the overlap between the two gene lists is plotted as -log10 transformed hypergeometric test p-values corrected for multiple testing by Benjamini and Yekutieli method. The range of the p-values is indicated in the color scale bar. Venn diagram illustrating the overlap between the differentially expressed genes in siLemd2- vs scrambled siRNA-transfected Bic-treated cortical cultures and Satb2CamkCre vs Satb2 floxed primary Bic-treated cortical cultures (Fisher's exact test, P value < 10E-16, OR = 3.159). Enrichment analysis for SATB2-bound genes in the LEMD2-regulated significant gene list (Fischer's exact test, P value < 10E-10, OR = 1.6).   "Volcano plots" of statistical significance against Log2 fold-change, depicting the PRGs (Tyssowski et al., 2018) that were differentially expressed in Bic-treated siLemd2- vs scrambled siRNA-transfected cultures (left panel) and Bic-treated Satb2CamkCre vs Satb2 floxed primary cortical cultures (right panel). The down regulated PRGs are indicated in blue (adjusted p-value < 0.05, Log2fold-change < -0.3) and the up-regulated (adjusted p-value < 0.05, Log2fold-change > 0.3) are shown in red.   Examples of IEGs with a SATB2 peak at their proximal promoter that were down-regulated in both Bic-treated Lemd2 knockdown and Satb2 knockout cultures.
Figure 2A. SDHA and SDHB silencing significantly increased AR full length protein levels in LNCaP, LAPC4, C4-2 and MR49F cells as well as both AR full length and V7 protein levels in 22Rv1 cells. B. ENZA acutely decreases AR levels (up to 18 h) while SDHB silencing rescued the early ENZA-mediated AR downregulation in LNCaP cells. C. SDHA/SDHB silencing maintains higher levels of AR transcriptional activity during acute phase of ENZA stress (18 h) in LNCaP cells. Data information: ENZA: enzalutamide.Data shown as mean ± SD of three independent experiments. Statistical analysis was performed using one-way ANOVA followed by Tukey's test *, p<0.05 and **, p<0.01 compared between groups. D. SDH repression during acute phase of ENZA stress increased transcription of different AR-regulated genes without altering AR mRNAs levels in LNCaP cells. Data information: ENZA: enzalutamide.Data shown as mean ± SD of three independent experiments. Statistical analysis was performed using two tailed unpaired Student's t-test *, p<0.05 and **, p<0.01 compared between groups. E-F. Overexpression of SDHA and SDHB subunits decreased AR protein levels (E) and AR transactivation (F) in LNCaP cells. Data information: ENZA: enzalutamide.Data shown as mean ± SD of three independent experiments. Statistical analysis was performed using one-way ANOVA followed by Tukey's test *, p<0.05 and **, p<0.01 compared between groups. G-H. LNCaP cell viability is increased by SDHA/SDHB silencing (G) and reduced by SDHA/SDHB overexpression (H) compared to siScr and empty vector, respectively. Data information: ENZA: enzalutamide.Data shown as mean ± SD of three independent experiments. Statistical analysis was performed using one-way ANOVA followed by Tukey's test *, p<0.05 and **, p<0.01 compared between groups.
Figure 4(A) Pressure-volume curves were determined using the FlexiVent system in age-matched control versus 3-month STZ induced diabetic mice. The curves represent group averages (mean ± SD; : p<0.05; N=5). (B) Quantitative analysis of static pulmonary compliance in age-matched control versus 3 months STZ induced diabetic mice, as described in Figure 3a. The curves represent group averages (mean ± SD; : P<0.05, : p<0.01; N=5). (C) Representative images of lungs from age (3- or 6- month) matched control versus STZ induced diabetic mice, stained for Masson's Trichrome stain, as described in Methods and visualized by bright field and polarized light, the accumulated ECM is recognized by its blue staining (Scale 40µm). (D) Percentage total lung capacity of controls versus patients with diabetes. The dotted line represents the cut-off decided as per the guidelines of the European Respiratory Society (ERS) and American Thoracic Society (ATS), (mean ± SD, : p<0.05; triplicates from each Ncontrol=44, Ntype-1=35, Ntype-2=110). (E) Percentage forced vital capacity of lungs in controls versus patients with diabetes. The dotted line represents the cut-off decided as per the guidelines of ERS and ATS, (mean ± SD; : p<0.05; triplicates from each Ncontrol=44, Ntype-1=35, Ntype-2=110). (F) Quantitative analysis of the NAD+/NADH ratio in lungs harvested from age-matched 3, or 6 months control, or STZ induced diabetic mice, after homogenization in extraction buffer (mean ± SD; : p<0.01, : p<0.001; N=5). (G) Quantitative analysis of the NAD+/NADH ratio determined in serum from patients with diabetes, as described in methods (N=3; mean ± SD, : p<0.01, : p<0.001).
Identification of proteins locally synthesized in synaptoneurosomes using high-resolution quantitative mass spectrometry and RNA-sequencing.Figure 2(A-D) Results of high-resolution quantitative mass spectrometry analysis identifying proteins with increased abundance in stimulated synaptoneurosomes. Volcano plots (Whitney-Mann test, Benjamini Hochberg correction, n=5 per group) showing abundance of identified proteins in NMDAR-stimulated (20 min) synaptoneurosomes as compared to unstimulated using iTRAQ8-plex (A) and TMT10-plex (B) labelling methods. Mitochondrial proteins are depicted in orange. The vertical line defines the p-value statistical significance cut-off. For nine mitochondrial proteins their mRNA abundance on polyribosomes was quantified, the data is presented on Figure EV2. (C) Biological functions of proteins identified as significantly upregulated after NMDAR stimulation (assembled from all three proteomic analyzes: LFQ, iTRAQ8, TMT10 (E) RNA absorbance profiles from polyribosomal fractionation of unstimulated and NMDAR-stimulated (20 min) synaptoneurosomes. Upon NMDAR stimulation, a fraction of mRNAs is shifted towards heavy-polyribosomal fraction, which represents actively translating ribosomes. The fraction of polyribosomes used for RNA-seq experiment is depicted. (F) Comparison of proteomic data with RNA-seq experiments on mRNAs associated with polyribosomes from synaptoneurosomal samples. Ribosome association of synaptoneurosomal mRNAs determined by normalizing RNA-seq values of polyribosome associated mRNA with total mRNA (y axis). Green dots represent mRNAs encoding proteins upregulated upon stimulation (identified in MS experiments) while orange dots represent mRNAs encoding mitochondrial proteins. Density curves for transcripts encoding mitochondrial proteins (orange) and upregulated proteins (green) detected by the mass spectrometry are present on the right side of the plot. Please note that both classes represent high abundant mRNAs with good ribosome association values. Transcripts with statistically significant increased or decreased abundance on the polyribosomes in response to the stimulation are depicted in red.
Thyrocytes display transcriptional heterogeneity (A) Dot plot depicting expression entropy on Y-axis against average gene expression on X-axis for the thyrocyte population.Figure 6(A) Dot plot depicting expression entropy on Y-axis against average gene expression on X-axis for the thyrocyte population. Each dot depicts a gene, with red dots depicting genes that show statistically significant (p-value < 0.05) difference in entropy from expected value. Expected value is represented by black regression line. pax2a and ctsba are marked on the graph. (B) t-SNE plot of the thyrocyte cluster with expression of tg, pax2a and ctsba. The color scale represents the normalized expression counts for each gene ranging from lowest (yellow) to highest (red). (B') Histogram overlaid with density plots depicting the distribution of normalized gene expression for tg, pax2a and ctsba.
a) Aversive associative memory performance in 3 min after training (STM) in 3-d-old female flies with pan-neuronal expression of UAS–Odc-1 (n = 7 independent experiments, F = 0.figf7(a) Aversive associative memory performance in 3 min after training (STM) in 3-d-old female flies with pan-neuronal expression of UAS-Odc-1 (n = 7 independent experiments, F = 0.04, one-way ANOVA with Bonferroni correction). (b) Aversive associative memory performance in 3 h after training (ITM), ARM and ASM of 3-d-old appl-driven UAS-Odc-1 female flies compared with control flies (n = 7 independent experiments; F = 1.95 for ITM, F = 0.10 for ARM, F = 1.05 for ASM; one-way ANOVA with Bonferroni correction). (c) Pan-neuronal expression of the UAS-Odc-1 in a wild-type background suppressed AMI in 30-d-old female flies (n = 7 independent experiments, F = 21.35, one-way-ANOVA with Bonferroni correction). (d) ITM, ARM and ASM of 30-d-old female flies with pan-neuronal expression of UAS-Odc-1 compared with their genetic controls (n = 7-8 independent experiments; F = 17.49 for ITM, F = 1.58 for ARM, F = 24.61 for ASM; one-way ANOVA with Bonferroni correction). (e) Expressing Odc-1 in just the mushroom body was sufficient to protect from STM decline in 30-d-old flies (n = 9-12 independent experiments, F = 9.25, one-way ANOVA with Bonferroni correction). (f) ITM, ARM and ASM of 30-d-old flies expressing mushroom body-specific Odc-1 compared with their genetic controls (n = 8-9 independent experiments; F = 11.73 for ITM, F = 0.50 for ARM, F = 16.6 for ASM; one-way ANOVA with Bonferroni correction). **P 0.01, ***P 0.001; ns indicates not significant, P > 0.05. Data are presented as mean ± s.e.m.
Figure 2A) Confocal microscopy time-series images of the increase in cytosolic Smac-GFP (magenta) in relation to the detection of RA-BAX/GB-DRP1 complexes (green) during apoptosis induction in MEF DRP1 KO cells. Scale bar 10 μm. Images are representative for n=3 independent experiments. B) Normalized fluorescence intensity of Smac-GFP in a region of interest in the cytosol and of RA-BAX/GB-DRP1 foci for individual cells (thin lines) and the average of all cells (thick lines, n=5). Time 0 min corresponds to the time point when RA-BAX/GB-DRP1 foci were detected. C) Quantification of BAX/DRP1 interaction (% cells with RA-BAX/GB-DRP1 foci normalized to the mito-BFP positive cells, n=100 cells per experiment) during inhibition of effector caspases (Q-VD-OPh), the mitochondrial permeability transition pore (CsA) versus control (DMSO), with or without apoptosis induction (+/- STS). Box plots represent the interquartile (box), median (line) and SD (whiskers). Significance was determined from n=3 independent experiments (with n=100 cells each) by paired two-tailed Student´s t-test (n.s. indicating p > 0.05) compared to DMSO control after apoptotic induction (STS).
Figure 3(A) Schematic illustration of STXBP4 protein, where the identified 9-amino acid sequence of STXBP4-WW domain was aligned across the indicated species. (B) STXBP4 forms a complex with several Hippo PY motif-containing proteins. Immunoprecipitation was performed with STXBP4 antibody. (C) The identified 9-amino acid sequence is required for the association between STXBP4 and AMOT. HEK293T cells were transfected with the indicated STXBP4 mutants and subjected to the pulldown assay. (D) Structural comparison between the YAP-WW1/SMAD7-PY and STXBP4-WW/SMAD7-PY complexes. The identified 9 amino acid residues were indicated for both complexes. (E) The YAP-WW1/SMAD7-PY and STXBP4-WW/SMAD7-PY complexes show similar cumulative average trend and average binding free energy (∆G) within standard deviation (the shaded region) of one another. (F) Loss of STXBP4 inhibits YAP phosphorylation and LATS activation. Western blotting was performed with the indicated antibodies. Loss of STXBP4 activates YAP. STXBP4 deficiency promotes YAP nuclear translocation (G) Loss of STXBP4 activates YAP. STXBP4 deficiency promotes YAP downstream gene transcription (mean ± s.d., n=3 biological replicates) (H). Scale bar, 20 μm.*** p < 0.001 (Student's t-test). (I) WW domain is required for the STXBP4-mediated YAP cytoplasmic translocation. STXBP4 KO cells were transfected with the indicated STXBP4 constructs and immunofluorescent staining was performed. HA-positive cells (arrows) from ~30 different views (~200 cells in total) were randomly selected and quantified for YAP localization. Percentage of HA-positive cells with nuclear YAP enrichment is shown. Scale bar, 20 μm. (J) Loss of STXBP4 attenuates YAP phosphorylation as induced by actin cytoskeleton inhibition. The indicated cells were subjected to serum starvation (treatment with no-serum medium for 12 hours), glucose starvation (treatment with no-glucose medium for 6 hours) or actin inhibition (treatment with 0.5 μg/mL latrunculin B or 5 μM blebbistatin for 30 min). YAP phosphorylation was detected using phospho-tag gel, where the YAP phosphorylation level was indicated.
Efficient MitoT to T cells underlies functional changes including enhanced immunosuppression through regulatory T cell (Treg) induction.Figure 4A Representative bright-field microscopy images of FACS-sorted CD4+ naïve MitoTneg (upper panel) and MitoTpos (lower panel) cells after 5 days in culture with plain media (no cytokines added). Red arrows are indicative of activation/proliferation clusters. B Representative FACS plots of Treg (CD127lowCD25+FoxP3+) populations after T cell differentiation on media with or without cytokines and antibody supplements (anti-CD3, IL-2 and TGF-b1). C FACS analysis of Treg induction after 5-7 days differentiation of FACS-sorted CD4+ naïve MitoTneg and MitoTpos cells in plain (n=5) or differentiation media (n=6) (Biological replicates, with different donors of PBMCs). D ICOS expression on FACS-sorted CD4+ naïve MitoTneg and MitoTpos cells after 5-7 days in culture with differentiation media. Representative FACS plot (left panel) and bar graph (right panel) of ICOS high population (n=4 biological replicates). E CCR7 expression on sorted CD4+ naïve MitoTneg and MitoTpos cells after 5-7 days in culture with differentiation media. Representative FACS plot (left panel) and bar graph (right panel) of CCR7+ population (n=4 biological replicates). F FACS analysis of Th1 (CD4+IFNγ+) induction after 5-7 days differentiation of FACS-sorted CD4+ naïve MitoTneg and MitoTpos cells in plain media (n=3 biological replicates). n/s= not significant.
HIF-1 is the main regulator of the differential gene expression pattern in Gpr124KO NPCs.Figure 3A, qRT-PCR analysis of NSC-specific markers (Fabp7, Hes5) and neuronal markers (Dcx, Tubb3) in the Prom1+ fraction, presented as fold change compared to the Prom1- fraction) from WT cortices at E14.5 (mean±SEM; N=3 for Dcx; N=6 for all other genes). B,C, Enrichment analysis for biological process gene ontology terms associated with the genes upregulated (B) or downregulated (C) in VZ cells from Gpr124KO embryos. D,E, Enrichment analysis showing the p-value of the target enrichment for upstream transcriptional regulators known to control the expression of the genes that were up-regulated (D) or down-regulated (E) in Prom1+ VZ cells from Gpr124KO as compared to control cortex. F, Western blot for HIF-1 (top), HIF-2 (middle) and a-tubulin as loading control (bottom) using forebrain lysates from E13.5 control (left) or Gpr124KOembryos (middle). HIF-1/2-transfected HEK293 cells served as positive control (right). G, Quantification of HIF-1 band intensities shown in panel F (mean±SEM; N=3; ** p<0.01). H,I, Immunostaining for HIF-1α (red) and DAPI (blue) in control (H, H', H'') and Gpr124KO (I,I',I'') cortices. Panels H',H'',I' and I'' are magnifications of the boxed areas in panels I and J, showing HIF-1α signal alone (H',I') or together with DAPI (H'',I''). Asterisks indicate autofluorescent blood cells. The dashed line indicates the basal boundary of the VZ. Scale bar = 100 µm. Full, dotted and dashed lines indicate basal and apical boundaries of the cortex or boundaries of the cortical zones, respectively. CP, cortical plate; IZ, intermediate zone; SVZ, subventricular zone; VZ, ventricular zone. Scale bar: 100 µm J, qRT-PCR analysis of HIF-1 target gene expression in VZ cells from the cortex of control and Gpr124KO E13.5 embryos (mean±SEM; N=4; *** p<0.001). SVZ, subventricular zone; VZ, ventricular zone.
Figure 5The macrophages from Atx∆ΜΕ/∆ΜΕ and Atx+/+ mice were stimulated with LPS (20 ng/mL, 20 min) The cell lysates were subjected to immunoprecipitation (IP), followed by immunoblotting (IB) analysis with the antibodies indicated. Presented is the representative from three independent experiments. Raw264.7 cells were stimulated by LPS with the ATX inhibitor (50 μM, 30 min) or vehicle (Veh, DMSO 0.1%) The cell lysates were subjected to immunoprecipitation (IP), followed by immunoblotting (IB) analysis with the antibodies indicated. Presented is the representative from three independent experiments. The macrophages from Atx∆ΜΕ/∆ΜΕ and Atx+/+ mice were stimulated with LPS (20 ng/mL, 20 min) The cell lysates were subjected to immunoprecipitation (IP), followed by immunoblotting (IB) analysis with the antibodies indicated. Presented is the representative from three independent experiments. Raw264.7 cells were stimulated by LPS with the ATX inhibitor (50 μM, 30 min) or vehicle (Veh, DMSO 0.1%) The cell lysates were subjected to immunoprecipitation (IP), followed by immunoblotting (IB) analysis with the antibodies indicated. Presented is the representative from three independent experiments. The macrophages from Atx∆ΜΕ/∆ΜΕ and Atx+/+ mice were stimulated with LPS (20 ng/mL, 20 min) The cell lysates were subjected to immunoprecipitation (IP), followed by immunoblotting (IB) analysis with the antibodies indicated. Presented is the representative from three independent experiments.