EMBO/sd-character-level-ner huggingface dataset:
Figure 1A Flow cytometric quantification of lymphocytes, monocytes, B-cells, natural killer (NK) cells, dendritic cells (DCs) and granulocytes in peripheral venous blood samples from non-diabetic (ND) and type-2 diabetic (T2D) patients with COVID-19. B Quantification of monocyte subpopulation phenotypes as classical (CD14Hi CD16-), intermediate (CD14Hi CD16+) or non-classical (CD14Lo CD16+). C Principle component analysis of lymphocyte and monocyte population frequencies in ND and T2D COVID-19 patients and in T2D patients without COVID-19.
Figure 3(A) Schematic overview for Conv-MAC formation. Bacteria were labeled with C5 convertases by pre-incubation with C5-deficient serum (Fig EV3). Following a washing step (@), convertase-labeled bacteria were incubated with uncleaved C5, C6, C7, C8 and C9 (termed 'Conv-MAC'). (B) Bacterial viability of convertase-labeled bacterial strains exposed to buffer (Conv) or C5-C9 (Conv-MAC). Data information: (B-E) Data represent mean ± SD of 3 independent experiments. (B, D, E) Statistical analysis was done using a ratio paired two-tailed t-test and displayed only when significant as * p≤0.05, ** p≤0.01, *** p≤0.001 or **** p≤0.0001. (C) Bacterial viability of convertase-labeled E. coli MG1655 exposed to a concentration range of C5 in the presence of 100 nM C6, 100 nM C7, 20 nM C8 and 100 nM C9. 'Ctrl' indicates bacteria that are pretreated with heat-inactivated ΔC5 serum. Dotted line represents the detection limit of the assay. Data information: (B-E) Data represent mean ± SD of 3 independent experiments. (D) Bacterial viability of convertase labeled E. coli MG1655 exposed to C5-C9 or conditions lacking one MAC component. As an extra control, convertase formation was blocked during ΔC5 serum incubation by adding 5 µM compstatin. Data information: (B-E) Data represent mean ± SD of 3 independent experiments. (B, D, E) Statistical analysis was done using a ratio paired two-tailed t-test and displayed only when significant as * p≤0.05, ** p≤0.01, *** p≤0.001 or **** p≤0.0001. (E) Bacterial viability of E. coli MG1655 exposed to FB depleted serum in the presence of 20 µg/ml OmCI (to deposit C4b and C3b without Bb). After washing, bacteria were exposed to C5-C9 in the presence or absence of C1 and C2 (to generate classical pathway C5 convertases, C4b2aC3b). Data information: (B-E) Data represent mean ± SD of 3 independent experiments. (B, D, E) Statistical analysis was done using a ratio paired two-tailed t-test and displayed only when significant as * p≤0.05, ** p≤0.01, *** p≤0.001 or **** p≤0.0001.
Figure 5Measurements of tumour volume of the respective cohorts (n = 6 animals per cohort). SM represents Birinapant. Error bars represent SD. The addition of either anti-CTLA-4 or anti-PD-1 antibodies prolonged survival in comparison to ILP-TNF/Mel/SM alone (n = 6 animals per cohort). SM represents Birinapant. Statistical analysis was performed with a log-rank test, * P ≤ 0.05. Tumours were collected 4 days after the ILP procedure and analysed by flow cytometry (n = 3 per cohort). The addition of anti-CTLA-4 antibodies led to a significant increase in CD4+ Foxp3- helper T cells (C) accompanied by a depletion of CD4+ Foxp3+ regulatory T cells (D). SM represents Birinapant. Tumours were collected 4 days after the ILP procedure and analysed by flow cytometry (n = 3 per cohort). The addition of anti-PD-1 antibodies led to an increase in Granzyme B (GzmB) expression on NK cells (E). SM represents Birinapant.
Figure 6After NEBD, Cyclin B2 localizes to unattached kinetochores, mediated by Mad2 bound to Mad1 or by Mad2 bound to a yet unidentified kinetochore receptor (protein-X). Multiple SAC factors, including kinases, localize at the outer kinetochores. Mad2-mediated Cyclin B2-Cdk1 contributes to SAC signalling, in complement with Mad1-mediated Cyclin B1-Cdk1. As a scaffold recruiting multiple SAC factors to the vicinity, the outer kinetochore catalyses the assembly of MCC. As a consequence, MCC inhibits the activity of APC/C to preclude the anaphase as long as improperly attached kinetochores are present. The error-correction machinery promotes the establishment of correct bipolar microtubule kinetochore attachment. When all kinetochores achieve bipolar attachment, SAC signalling is silenced, and the cell enters anaphase. C: C-Mad2, O: O-Mad2, X: protein X, B1: Cyclin B1, B2: Cyclin B2
Figure 2(A) Scheme for the preparation of DY-635 targeted liposomes containing the PI3Kγ inhibitor AS605240 (T-LipoAS). LC-MS determined concentrations of AS605240 and DY-635 individually prepared batches used for all subsequent experiments. The graph depicts the mean ± SD from five different batches. (B) Hydrodynamic diameters of different liposomes in histidine buffer were analyzed by dynamic light scattering. The graph depicts representative plots obtained from dynamic light scattering in Histidine buffer. Further, all batches in this study have been analyzed for size by the manufacturer using DLS and were confirmed to be stable in solution for at least one year. (C) Uptake characteristics of T-LipoAS by primary human hepatocytes demonstrate competitive inhibition by cyclosporin A- and energy dependence, confirming active uptake by organic anion transporters (OATPs). The data points are depicted mean ± SD from two batches of primary human hepatocytes in quadruples. (D) T-LipoAS plasma disappearance rate in murine ear veins and estimated half-life obtained by intravital microscopy. The mean fluorescence intensity averaged between the remaining 24 regions of interest (from n = 4 FVB/N mice) and the positive standard error depicted in the figure. (E) Quantification of AS60524060 min after injection of 1 mg kg-1 AS605240 (i.p. in DMSO, n=4 animals) or 2.5 mg kg-1 T-LipoAS (i.v. n=5 animals) in tissue lysates quantified by LC-MS. Bars depict the mean + SD for each group. *p<0.05 for Wilcoxon test between T-LipoAS and AS605240 in each tissue. (F) T-LipoAS effectively inhibits fMLP-stimulated PI3Kγ, reflected by inhibiting AKT S473 phosphorylation activity in hepatocytes from three different batchtes. The mean pAKT/AKT ratio and standard deviation (SD) were calculated for all experiments separately. (G) Episcopic imaging of mice treated with T-LipoAS for 15 or 60 min and relative concentration of the targeting moiety DY-635 in the different compartments. (H) Intravital microscopy to monitor T-LipoAS kinetics in the liver. Liposomes appear in the sinusoidal vasculature after 5-15 minutes and accumulate within hepatocytes. After 35-60 min, the bile canalicular system appears stained, indicating the processing and elimination of the targeting moiety (DY-635) from T-LipoAS. Similar distribution patterns had been observed in all repetitions (n=7).
Sporozoite budding is impaired in α1-tubulin(-) parasites A.Figure 2Electron micrographs showing different stages of development in WT and α1-tubulin(-) parasites. Key structural elements are highlighted in the following colors: blue: plasma membrane; yellow: inner membrane complex; green: microtubules; light blue: micronemes; lilac: rhoptries; brown: rootlet fiber; cyan: nucleus. Note the undulating shapes of the elongated mutants and that micronemes are hard to distinguish from other small vesicles in the α1-tubulin(-) parasites. The rootlet fiber in panel II starts at the apical tip and in panel V is associated with the centriolar plaque (dark structure in nuclear envelope). Panel III corresponds to Fig 1D. Scale bars: 200 nm. 3D reconstruction from serial sectioning reveals that growing α1-tubulin(-) 'sporozoites' lack apical polarity and fail to pull in nuclei. Microtubuli: green; rootlet fiber (connecting apical pole to centriolar plaque): red; rhoptries: purple; endomembraneous vesicles (Golgi, premicronemes): brown; nucleus: cyan; sporozoite plasma membrane and inner membrane complex: blue; dotted lines show location of sporoblast membrane. 17 and 10 sections of 100 nm and 300 nm thickness were processed for the tomograms in WT and α1-tubulin(-) parasites, respectively. Scale bar: 1 µm. Tomography of serial sections from budding α1-tubulin(-) parasites at day 13 (same as in panel B) and day 17 to highlight the increase of surface area (blue) with time. The oocyst wall at day 17 is highlighted by cyan lines (top), the sporoblast membrane is highlighted by red lines (bottom). The sporoblast membrane at day 13 is indicated by a dashed line (red). 10 and 11 sections of 300 nm thickness were processed for the tomograms at day 13 and day 17, respectively. A single continuous parasite was highlight at day 17. Scale bar: 1 µm. α1-tubulin(-) parasites show multiple attachments (arrowheads) with the sporoblast membrane at day 17 post infection. Note the highly branched nature of the budding parasite (same parasite as in panel C) shown in two views in I and II. Right: slices through the tomogram in grey scale with the outlines used for the 3D model indicated. Two connections with the sporoblast are indicated by 1 and 2. Scale bars: 1 µm.
Fig.Figure 1A Chemical structure of XMU-MP-5. B Antiproliferative activities of XMU-MP-5 and crizotinib against EML4-ALK Ba/F3 and parental Ba/F3 cells, respectively. Cells were treated with increasing concentration of each drug for 48 hours and then analyzed by MTS assay. Each concentration was performed in triplicate. Data were presented as Mean ± SEM from three independent experiments (n = 3) . C XMU-MP-5 downregulates ALK signaling pathways in EML4-ALK Ba/F3 cells. Cells were treated with XMU-MP-5 or crizotinib for 4 h, and then analyzed by immunobloting. D The KINOMEscan result of XMU-MP-5 against a panel of 468 kinases. Selectivity score S(10) and kinase hits of XMU-MP-5 with ctrl% ≤10% were shown. ALK and its mutants were highlighted in blue (see Appendix Table S1 for the full list and see Experimental Section for the detailed kinase group names).
Figure 8(a) MCL1 Western blot in protein extracts from Vil Apc and Vil Apc Huwe1hom tumours. Levels of MCL1 protein are significantly increased in tumours lacking HUWE1 (Mann Whitney, p = 0.04, n = 3). (b) Kaplan-Meier survival plot of cohorts of induced Lgr5 Apc Huwe1 and Lgr5 Apc Huwe1 Mcl1 mice. Deletion of one copy of Mcl1 led to a significant increase in survival of these animals (Log Rank, p = 0.0052, n = 9 vs 10). (c) Ratio of adenoma / indolent lesions observed in Lgr5 Apc Huwe1 and Lgr5 Apc Huwe1 Mcl1het mice. Note the decreased ration of adenoma / indolent lesions observed upon Mcl1 deletion (Mann-Whitney, p=0.0281, n = 8 v 8). (d) Schematic outlining the tumour suppressive role of HUWE1. When HUWE1 is expressed amount of MYC, γH2AX and MCL1 are maintained at low levels. Following HUWE1 mutation or loss MYC, γH2AX and MCL1 leading to increased levels of proliferation and DNA damage. This leads to loss of Apc and tumour initiation. Increased MCL1 is critical to protect these cells from apoptosis induced by the high levels of DNA damage.
FRAP reveals dynamics of concavin-GFP and stasis of PhiLl1-GFP A, B.Figure 3A, B. Time series of concavin-GFP (A) PhiL1-GFP (B) sporozoites before and after bleaching and quantification of the fluorescence signal over time of 3 technical replicates. * indicates time of bleaching. Shown is the mean ± SD. C. Super resolution (STED) imaging of PhiL1-GFP and CSP as well as concavin-GFP and CSP. Cells were stained with an anti-GFP antibody in combination with Atto-594 (green) in addition to an anti-CSP staining in combination with Atto-647. Images were deconvolved using the Richardson-Lucy algorithm. The distance between the 2 signal peaks was measured using the plot profile of the respective channels in Fiji. Data points represent distance in individual sporozoites at the center of the cell from 2 independent biological replicates. P-values are calculated using the Kruskal Wallis test followed by the Dunns multiple comparison test. Scale bar: 1 µm. D. Localization of PhiL1-GFP (green) in concavin(-) parasites. Nuclei (blue) stained with Hoechst. Scale bar 5 µm. E. Localization of SiR-Tubulin (red) in concavin(-) parasites. Nuclei (blue) stained with Hoechst. Scale bar 5 µm. F. Localization of CSP (red) in concavin(-) parasites. Nuclei (blue) stained with Hoechst. Scale bar 5 µm. Data information: Asterisks in D-F indicate apical part of the sporozoite.
Figure 7(A) Four databases used in Fig 1A were intersected with human TFs database JASPAR to identify differentially expressed TFs in LUAD. The Venn diagram depicts the overlap between 5 independent data sets. (B) Listed are twenty-five LUAD-related differentially expressed TFs. TFBSTools was used to predict potential binding sites of each TF in QKI-5 promoter sequence (position -3000 to +200). TFBSTools minscore > 95%; TFs, transcription factors. qRT-PCR analyses of mRNA expression of ten TFs in A549 cells transfected with siRNAs of TFs, which have potential binding sites in QKI-5 promoter. qRT-PCR analyses of mRNA expression of QKI-5 in A549 cells transfected with siRNAs of TFs, which have potential binding sites in QKI-5 promoter. (E) Western blot analysis of QKI-5 protein levels in KLF6-silenced A549 cells. (F) An overview of KLF6-ChIP-seq data (GSE96355) is illustrated using Integrative Genomics Viewer (IGV) software. An obvious peak was detected at position -100 to +100 in the QKI-5 promoter. (G) Upper panel: computational algorithms using PROMO and JASPAR predicted that two putative KBEs were harbored in ΔQP region (position -400 to +200). QP, QKI-5 promoter; KBE, KLF6 binding element. Lower panel: anti-KLF6 ChIP was conducted in A549 cells and followed by PCR and gel-staining to confirm the presence of QKI-5 promoter sequence containing KBE1 (position -346 to -336) or KBE2 (position +21 to +31). The input and anti-IgG antibody were used as positive and negative controls, respectively. (H) Left panel: schematic drawing shows the pGL3-ΔQP luciferase reporter assay system. Boxed areas indicate four ΔQP segments containing wild-type or mutants of KBE1/2 (Mutant 1, Mutant 2, and Mutant 1*2). Right panel: four different pGL3-ΔQP luciferase reporter constructs were co-transfected with si-NC or si-KLF6 into A549 cells, and their luciferase activities were determined qRT-PCR analysis of KLF6 mRNA in 61 LUAD tissues and matched paracarcinoma tissues (I) T, LUAD tissues; N, paracarcinoma tissues. Y axis represents the log10 transformed fold change of mRNA expression of KLF6. Central dotted line of the violin plot represents median, and upper and lower dotted line represents quartile (I). T/N mRNA expression of KLF6 in 61 paired LUAD tissues (J). T, LUAD tissues; N, paracarcinoma tissues. Y axis represents the log10 transformed fold change of mRNA expression of KLF6. (K) Correlation between KLF6 and QKI-5 mRNA expression in 61 paired LUAD tissues. X and y axes represent the log10 transformed fold change of T/N expression ratios of KLF6 and QKI-5 mRNA, respectively. P = 0.002 by Pearson's correlation test. (L) A proposed work model: KLF6/QKI-5/TGFβR1 axis regulates TGF-β/SMAD signaling during TGF-β-induced EMT.
Figure 5A. Schematic representation of the in vivo experimental design. B. Effect of JQ1 and Salinomycin treatment on the tumor growth of CRCM434 (n=10) The grey area corresponds to the period of drug treatments. C-E. Quantification of the proportion of residual ALDHbr cells in treated PDX normalized to the proportion of ALDHbr cells in the vehicle-treated tumors, measured by flow cytometry. Statistical test used is a student t-test. Data represent mean ±SD (n=10). Quantification of the proportion of residual ALDHbr cells in treated PDX normalized to the proportion of ALDHbr cells in the vehicle-treated tumors, measured by flow cytometry. Statistical test used is a student t-test. Data represent mean ±SD (n=10). Reimplantation assay (CRCM434). Two-week treated PDXs were reimplanted, in serial dilutions, into new recipient mice and tumor growth was monitored Each curve represents the growth kinetic from one individual injection. G-I. Bar plots displays bCSC frequency calculated using an extreme limiting dilution analysis (ELDA). Results are expressed as the estimated number of bCSCs for 10,000 tumor cells. Statistical test used is Pairwise chi-square test. J-L. Effect of JQ1 and Salinomycin treatments on the metastasis formation of CRCM404 and CRCM434. Metastasis formation was monitored using bioluminescence imaging in the treated mice livers and lungs (J). Quantification of the normalized photon flux revealed a statistically significant decrease in metastasis formation in Sal/JQ1 treated mice compared to the control mice (K, CRCM404, p=0.04; L, CRCM434, p=0.02). Statistical test used is a Wilcoxon test. Error bars represent mean ± SD (n=10).
Quantitative real-time PCR (RT–qPCR analysis of the relative mRNA abundances of Glut1, Glut3, Hk2 and Gapdh in WT and Pink1 KO mice MEF (a) or neurons (c).f2Quantitative real-time PCR (RT-qPCR analysis of the relative mRNA abundances of Glut1, Glut3, Hk2 and Gapdh in WT and Pink1 KO miceMEF (a) ß-Actin mRNA was used for normalization, and the Pink1 KO data are expressed as the change relative to WT. Western blot analysis of the protein abundances of PINK1, GLUT1, GLUT3 (not detectable in MEF), HK2, GAPDH and HIF1α in WT and Pink1-null mice MEF (b) ß-Actin was used as loading control. Quantitative real-time PCR (RT-qPCR analysis of the relative mRNA abundances of Glut1, Glut3, Hk2 and Gapdh in WT and Pink1 KO neurons (c). ß-Actin mRNA was used for normalization, and the Pink1 KO data are expressed as the change relative to WT. Western blot analysis of the protein abundances of PINK1, GLUT1, GLUT3 (not detectable in MEF), HK2, GAPDH and HIF1α in WT and Pink1-null neurons (d); ß-Actin was used as loading control. (e) Western blot against PINK1, GLUT1, GLUT3 and HIF1α in WT and Pink1 KO mice skeletal muscle samples; α-Tubulin was used as loading control. Only representative western blots are shown per condition; the replicates and the semi-quantitative estimation of the band intensities are shown in the Supplementary Information. The mean±s.e.m. values of the mRNA data were calculated from the fold change of each ß-Actin-normalized transcript abundance in the Pink1 KO samples versus that in the WT. Thus, in all cases, the WT values were considered=1.00. *P0.05 versus the corresponding WT (Student's t-test; n=3-4 independent experiments).
a) Lysates from cells expressing the indicated FLAG-tagged F-box proteins (FBPs) were used in binding reactions with beads coupled to either a peptide or a phospho-peptide (sequences shown on top of the panel).figf4(a) Lysates from cells expressing the indicated FLAG-tagged F-box proteins (FBPs) were used in binding reactions with beads coupled to either a peptide or a phospho-peptide (sequences shown on top of the panel). Beads were washed with lysis buffer, and bound proteins were eluted and subjected to SDS-PAGE and immunoblotting. ( (b) Denatured extracts from HEK293T cells stably expressing either FLAG-tagged wild-type p85β or FLAG-tagged p85β(Y655A) were immunoprecipitated (IP) with either an anti-FLAG resin or a 4G10 platinum resin and immunoblotted (IB) as indicated. Immunoblots of whole-cell lysates (WCL) are also shown in the last two lanes. (c) Denatured extracts from HEK293T cells expressing either FLAG-tagged wild-type p85β or the indicated FLAG-tagged p85β mutants were immunoprecipitated (IP) with an anti-FLAG resin and immunoblotted as indicated. Uncropped images of blots are shown in Supplementary Fig. S8.
Fig.Figure 3Unsupervised hierarchical clustering based on the average degree of methylation of the 500 most variable promoters (red - low/violet -high methylation levels); * - relapse (REL) sample of patient P4 with blast content of 8% The degree of the mean promoter methylation in patients' samples plotted against the degree of mean promoter methylation in PDX samples; ρ - Spearman's rank correlation coefficient; median combined ranks across hexagonal bins are shown as a gradient according to the color legend
Antagonists display inhibitory efficacy on agonist‐responsive ARBEsHeat map showing raw tags distribution over the four types of agonist‐responsive ARBEs in LNCaP cells treated with vehicle, bicalutamide (10 μM), bicalutamide plus DHT (10 nM), enzalutamide (10 μM), or enzalutamide plus DHT (10 nM).Figure 5A Heat map showing raw tags distribution over the four types of agonist‐responsive ARBEs in LNCaP cells treated with vehicle, bicalutamide (10 μM), bicalutamide plus DHT (10 nM), enzalutamide (10 μM), or enzalutamide plus DHT (10 nM). The order of sequences in each type of ARBE is the same as the order of sequences shown in Fig A. B UCSC genome browser views of sequencing data at KLK3 locus under different conditions. C Regular ChIP analysis of AR on KLK3 enhancer. LNCaP cells were treated with or without agonist and antagonist for 4 h. The data are presented as the fold enrichment over IgG (mean ± SD, n = 3). D Quantitative RT‐PCR was performed to assess KLK3 mRNA levels under agonist or antagonist treatments. The data are the mean of triplicates ± SD. E Eight agonist‐responsive ARBE reporter constructs used in Fig B were transiently transfected into LNCaP cells. Cells were stimulated with vehicle, DHT (100 nM), bicalutamide (10 μM), bicalutamide plus DHT, enzalutamide (10 μM), or enzalutamide plus DHT for 16-24 h, and luciferase activities were measured. The results are presented as the mean ± SD of the quadruplicate transfections.
Figure 2Reporter gene assays addressing expression of lacZ fusions under GlcN6P replete and depletion conditions. strains were grown in 96-well plates and exposed to various degrees of GlcN6P depletion elicited by Nva-FMDP. Cells were harvested at indicated times and the β-galactosidase activities were determined. Strains Z197 and Z360 were used, which harbor glmY'-lacZ and glmZ'-lacZ fusions, respectively. Reporter gene assays addressing expression of lacZ fusions under GlcN6P replete and depletion conditions. strains were grown in 96-well plates and exposed to various degrees of GlcN6P depletion elicited by Nva-FMDP. Cells were harvested at indicated times and the β-galactosidase activities were determined. Expression of glmY'-lacZ in strain Z197 and the ∆rapZ mutant Z225 is compared. Reporter gene assays addressing expression of lacZ fusions under GlcN6P replete and depletion conditions. strains were grown in 96-well plates and exposed to various degrees of GlcN6P depletion elicited by Nva-FMDP. Cells were harvested at indicated times and the β-galactosidase activities were determined. Strains Z190 and Z201 were addressed, which transcribe glmY'-lacZ either from the σ54-promoter or the σ70 promoter, respectively. Reporter gene assays addressing expression of lacZ fusions under GlcN6P replete and depletion conditions. strains were grown in 96-well plates and exposed to various degrees of GlcN6P depletion elicited by Nva-FMDP. Cells were harvested at indicated times and the β-galactosidase activities were determined. Strains Z190 and the ∆qseF mutant Z196 are compared, both of which transcribe the glmY'-lacZ fusion solely from the σ54 promoter. Reporter gene assays addressing expression of lacZ fusions under GlcN6P replete and depletion conditions. strains were grown in 96-well plates and exposed to various degrees of GlcN6P depletion elicited by Nva-FMDP. Cells were harvested at indicated times and the β-galactosidase activities were determined. Complementation experiment analyzing the requirement of rapZ for glmY expression in cells grown to exponential phase under standard conditions in flask cultures. Strains Z197 and the ∆rapZ mutant Z225 were used. Tested plasmids were pFDX4291 (vector control for pFDX4324 and pYG82 = VC1), pFDX4324 (rapZ), pYG82 (rapZquad), pBGG237 (vector control for pBGG164 = VC2) and pBGG164 (strep-rapZ).