EMBO/sd-character-level-ner huggingface dataset:
A. Schematic of the targeting vector. In the vector, the RIBEYE-specific A-domain (yellow) is fused to the genetically encoded Ca2+-sensor GCamP3 (green), followed by a stop codon and the Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE, blue) and an PGK-neomycin resistance cassette (orange) that is flanked by frt-sites (red ovals). This entire DNA sequence is flanked by loxP-sites (dark red triangles). After homologous recombination into the RIBEYE locus (RBEKI+neo), Flp-recombinase (introduced via transgenic expression) removes the selection cassette to generate the RBEKI allele. Subsequently, Cre-recombinase excises the entire A-domain and its accompanying sequences to produce the KO allele (RBEKO). Selected restriction sites are shown.
Representative immunofluorescence images of gastric chief cells after vehicle or 24h HDT treatment stained for Pepsinogen C (PGC, red, granules) and MAP1LC3B (green, autophagy marker). Top row is wild-type, bottom row is Atf3−/−. Scale bar, 50μm. Stomach unit base outlined by dashed white line.
A, Normalized weight of Ssrp1fl/fl; CreERT2+/+ mice of different ages (weeks) after the start of tamoxifen (TMX) treatment. A. Mean weight (%) ± SD. P < 0.05 for all tamoxifen treated groups versus vehicle (ANOVA). Log-rank test p = 0.032 for the oldest male age group versus all other male groups; p = 0.013 for all females versus all males; for all other comparisons p > 0.05. n = 6-10 mice.
E-F) Heatmaps showing grade specific, TSS-distal (E) or TSS-proximal (F) acetylated peaks and their relation to other histone marks. The box-plots indicate the signal intensity for each of the modifications (normalized values were transformed into a 0-1 range; central values represent the median).
C NRVMs and neonatal cardiac fibroblasts (CFs) were serum-starved, pretreated with vehicle or 200 nM L798106 (EP3 receptor antagonist) for 20 minutes, and were stimulated with 1 μM PGE2 for 10 minutes. PAK2 and PKD phosphorylation was assessed by immunoblot. Calsequestrin was used as a myocyte-marker Data information: In (A-C) representative images from 3 independent experiments are shown
WT and SNX10 KO Caco-2 cells were treated with or without OMVs (100 μg/mL) for 24 h. quantiﬁed the percentage of Snail (E) or Slug (F)-positive nuclei respectively. Data are means ± SD. One-way ANOVA followed by Bonferroni post hoc test was used for statistical analyzes. ***p < 0.001.
(A) NIH-3T3 cells were transduced with retroviral vectors expressing M45 or GFP. Two days after transduction cells were stimulated with the TLR4 agonist LPS (10 µg/ml), the TLR2 agonist LTA-SA (10 µg/ml), or IL-1β (20 ng/ml). IκBα levels were determined by immunoblotting.
C miR-150 levels in TGFβ-treated WT (IRE1α +/+) and IRE1α -/- MEF cells. *P = 0.018. Results are expressed as fold change compared to the Ctrl.
(B) The ability to protect S. aureus USA300 from intracellular killing by gentamicin is shown. Here, experiments were performed as in (A) except during the initial gentamicin treatment (100 μg/mL for 1h) to kill extracellular bacteria macrophages were also treated with either DMSO or PIK-III/Dynasore to inhibit fluid phase uptake. At 1.5 h post-infection cells were washed and treated with gentamicin (300 µg/mL) in the presence of either DMSO (vehicle) or PIK-III + Dynasore which were maintained throughout the experiment. The data are presented as the mean number of surviving bacteria in CFU/mL at 10 h post-infection +/- standard deviation. These data derive from a total of 15 biological replicates of S. aureus from at least three independent experiments. *** p<0.001 and statistical significance was determined by an unpaired two-tailed t-test with a Welch's correction.
a, Expression levels of ISX, TWIST1, Snail1, Fibronectin (FN1), VEGF, and E-cadherin (CDH1) mRNA were examined in a ISX-GFP inducible Tet-ON transformants at 8 h after addition of DOX. Data are presented as mean ± SD in graph (p< 0.001 compared to time point 0h; Student's t‐test) of 3 independent experiments, each performed in triplicate.
Binding of β-IgI3 coupled to Streptavidin-PE to DB coated with rCC1-N wildtype or variants. Mutation of CC1-N residues 29, 44, 89, 91 and 95 lead to significant changes in β-IgI3 binding capacity.
I. Quantification of the Um/G and Cm/G ratios in endogenous tRNAs isolated from WT and hTrmt13 KO cells. Quantification was performed by comparison with the standard curve obtained from pure nucleoside standards running in the same batch. Statistical analysis was performed using t-tests. Error bars represent mean ± SD for three independent experiments.
Schematic representation for the generation of ArCK cells. Time 0 is defined by the estimated onset of Mps1 inhibitor-induced chromosome mis-segregation.
D ROC analysis confirmed the increase in performance of the LC score based classification on the validation set of EBCs (black line) over a classification relying only on Em/Ad expression ratios of GATA6 (pink line) or NKX2-1 (blue line). The orange diamond represents the optimal operating point of the SVM classifier, i.e. the point on the curve with maximal Youden´s J index.
A. Distribution of Oct4, Nanog, Sox2, Suz12 and Pol II ChIP-seq reads around the transcription start sites (TSS) of the mESC-specific SATS (left) and common (right) isoforms in mESCs.
(A) MG1655 WT, single mutants of pstA and ugpB, and a double mutant of pstA ugpB were transformed with pBR322 and various pBR322-based folding biosensor constructs. The transformants were examined by a spot titer assay on LB agar plates containing various ampicillin concentrations. Strains containing pBR322 bla::Im7 L53A I54A gain considerable ampicillin resistance in the presence of a pstA mutation (compare uppermost left and right panels). This resistance is completely lost upon transducing in a ugpB mutation (compare next panels down), showing that ugpB is responsible for the resistance gained by the pstA mutation.
The density of NPC detected by TEM in the 5DO dTorKO NE. Each point shows the mean of multiple measurements from an individual nucleus, bars show mean ± SD for the group (n = 5). One-way ANOVA, with Bonferroni's post hoc test. ** p < 0.01, *** p < 0.001 and **** p <0.0001.
(D) Macrophages were transduced with shNS or ATG13 shRNA (shATG13) and analyzed for ATG13 expression. Bottom, a representative blot is shown. Top, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4.
qRT-PCR gene expression analysis showing the fold-change of select DNA-damage response-genes panel in Molm-14-xenograft-derived: (E) Primary recipient KSL, n=6 Data indicated by bars of fold-change calculated relative to matching controls, normalized to the endogenous control Gapdh and presented as means ± SEM.
53BP1-RFP cells, in which the endogenous 53BP1 gene locus had been engineered by CRISPR/Cas9 to express 53BP1-mScarlet from the natural promoter, were treated with NCS (25 ng/ml) and imaged at 30 minutes intervals. Examples of 53BP1 fusions (green arrowheads and magnified regions) and fissions (blue arrowheads and magnified regions) are shown on the left and in higher magnification on the right.
A. Accumulation of Cy3-labeled oligo#5 in the area around the 3rd ventricle one hour post injection, shown is the ventral part of a coronal section -1.34 mm from Bregma. The injection coordinates were AP: -1.82 mm, DV: -4.5 mm, ML: 0.B. Uptake of oligo#5 in the arcuate nucleus region (arc), enlarged from panel A.
B. Peptides are displayed on major coat protein p8 or minor coat protein p3, pre-adsorbed on non-target mATG8 (purple box) and selected on target mATG8 (blue box). Specific peptides are identified by ELISA and subsequently sequenced (green box). Efficacy and specificity of the selected sensors is determined by pull-downs, intracellular co-translocation, peptide binding-arrays and cellular assays. Sensors are further improved by rational optimization of avidity and binding affinity.
(C) Wing phenotype induced by depletion of B52 in the posterior domain of the wing disc combined with modulation of Hpo pathway. Dotted lines separate anterior (top) and posterior parts (bottom) of the wing. Flies were grown at 18°C.
Left panels: representative images of the heart of wild-type and Tchp knock-out mice stained for CD31 (green) and p62 (magenta). Scale bars, 100µm, and 50µm for the inset. Right panels: Quantification of the percentage of cardiac area (n=4 mice per group; unpaired t-test; **p=0.083 vs wild-type) or vessels positive for p62 (n=4 mice per group; unpaired t-test; **p=0.058 vs wild-type) and vessel density (n=4 mice per group; unpaired t-test; **p=0.0097 vs wild-type).
A - D Clustering of metabolome data in patients and controls; PLS-DA plots; VIP score plots of top 15 metabolites; volcano plots of all metabolites in blood of MELAS/MIDD (D). Data information: Colours in VIP score and volcano plots indicate the same most relevant and/or significantly changed metabolites among all patients groups. C3, component 3 HIAA, 5-Hydroxyindole-3-acetic acid; SDMA, symmetric dimethylarginine; TCA, taurocholic acid.
Left: Schematic diagram of manufacturing polyacrylamide gels with stiffness gradient. The gel containing photoinitiator is solidified by ultraviolet light irradiation. Mask with a constant speed is used to control the irradiation time for a hardness gradient. Right: Representative stiffness gradient of polyacrylamide gels measured by atomic force microscope was plotted (34 kPa/mm and 29 kPa/mm respectively).
(c) Luciferase activity was measured after transfecting increasing amounts of TFEB-FLAG in combination with Pgc-1α WT or Pgc-1α DEL plasmids. Bar graphs represent mean ± s.d. of n = 3independent experiments, ****P≤0.0001 compared with mock transfected cells.
B. Gene Ontology cellular component (GOCC) term enrichment analysis of proteins with upregulated ubiquitylation sites. The bar plot indicates terms that showed a significant enrichment (p<0.001)
(E) lncPSCA-knockout significantly promoted growth of MGC80-3 (n = 8) or HGC-27 (n = 7) xenografts compared with control xenografts after 27 or 18 days.
(C) Tumor volume in mice treated or not with LPS and/or FTY720 according to the scheme.
Heat maps and unsupervised hierarchical cluster analyses of the >2 fold upregulated genes in Dhigh
B Representative images for CO-FISH on metaphase spreads in wild type (WT) Hela and U2OS cells. The leading strand telomeres were labeled by PNA-FISH with a (TTAGGG)3-Alexa488 probe (green), the lagging strand with a (CCCTAA)3-Cy5 probe (pink), and the DNA was stained with DAPI. Examples of telomere sister chromatid exchange (t-SCEs) events are marked with white arrows. Scale bar: 5µm
C RT-qPCR expression analysis of selected miRs in U87FO cells grown 48 h in the presence (+) or absence (-) of Dox (n = 3; mean ± SD). Expression levels were normalized using U6RNA as control. Expression levels in non-induced cells were set as 1.
Extracellular flux analysis in human fibroblasts showing differences in OCR (oxygen consumption rate) and ECAR (extracellular acidification rate) by genotype. Oligom; Oligomycin, FCCP; Carbonyl cyanide-ptrifluoromethoxyphenylhydrazone, 2-DG; 2-deoxy-glucose. Quantification of baseline OCR and ECAR is shown, as well. n=3 per genotype with four technical replicates.
C, D. HUWE1-knockout 293T (C) and HeLa (D) cells show increased DNA breaks in the absence of exogenous DNA damage treatment. Results from the Alkaline Comet Assay are shown. The "n" numbers of comet tails analyzed (pooled from two independent experiments), as well as the mean, are indicated on the graphs. HUWE1-knockout HeLa cells did not show increases breakage in the Neutral Comet assay (Fig EV1B), indicating that the majority of breaks observed in cycling HUWE1-knockout cells are not double strand breaks, but rather single strand breaks and other types of lesions.
(K) Hot plate test.. n = 8 for WT mice, n = 12 for KO mice. **, p<0.01, One-way ANOVA with Bonferroni's post hoc test (F(1, 18) = 17.51). Data are presented as mean ± SEM.
RT plus anti-PD-L1 (C) increases CD8:Treg ratio. Bar graphs show ratio of CD8:Treg ratio in tumor samples based on flow cytometry analysis, as indicated (n=5 per group; means ± SD, n=1, One-way ANOVA, Bonferroni test).
Structural model of βarr1 in complex with phospho-peptides corresponding to the V2R, B2R and B2RL370T were generated based on previously determined structure of V2Rpp-βarr1 complex (middle panel). A bifurcated salt bridge links the V2R and B2RL370T peptides to K294 in the lariat loop of βarr1 via T359/T360 and T369/T370, respectively, but not in B2RWT peptide (upper panel). The frequency of salt bridge formation between the phospho-sites on the receptor and K294 in βarr1 was computed over 4 μs accumulated simulation time per complex using a distance threshold of 3.2 Å between the oxygen of the phosphate group of phosphorylated threonines and the protonated nitrogen of K294. B2RL370T mutant establishes a bifurcated interaction with K294 in the lariat loop, analogous to that in V2R peptide while B2R peptide forms only a single salt bridge (Figure 6, lower panel). Differential lariat loop stabilization correlates with distinct conformational states. Simulations of 4 μs per complex were clustered with a rmsd cutoff of 2.2 Å yielding "Cluster 1" and "Cluster 2" while "None" reflects conformations that did not fulfill this condition. The phospho-peptides corresponding to V2R and B2RL370T with a conserved bifurcated salt bridge adopt preferential conformational states belonging to "Cluster1" the B2RWT peptide with a single salt bridge favors the conformations of "Cluster 2"
Pearson correlation coefficients and correlation P‐values were calculated evaluating TF gene expression levels in iPSC‐derived DAn from PD patients and controls (n = 14) under a 2‐tailed Student's t‐test. Among TFs showing coordinated expression, maximal correlation was observed for FOXA1, FOXA2, NR3C1, HNF4A, and FOSL2.
C. Calculated IC50 values for reduced growth of PeTa, WaGa, MS-1, MKL-1 as well as HDFB controls based on Fig 1B and Fig EV1A.
Differentiated lung bud tip organoids at air-liquid interface in co-culture with donor-specific human fetal lung fibroblasts. After 14 days of differentiation at air-liquid interface, cells express HTI-56, green, markers in areas containing one cell layer. Dotted lines indicate the barrier between multilayered and single layered epithelium. Data information: Nuclei are stained with Hoechst Scale bars indicate 50 μm.
C ALS-linked PDIA1 variants were generated as recombinant proteins and then analyzed by circular dichroism (CD). Averages for CD spectroscopic scans of PDIA1WT and mutants are shown.
Adult mouse back skin sections from different postnatal (P) days immunostained for LYVE1 (red), Lhx2 (green) and counterstained with DAPI (blue). n= 3 - 4 skin samples per mouse, n= 3 - 4 mice. Scale bar, 50 μm. epi, epidermis; der, dermis.
B Quantitative RT-PCR of the indicated cell lines with the indicated knockdowns. For RSRC2 and SRSF2 the ratio of NMD isoform to canonical isoform was calculated. Data points and means are plotted as log2 fold change (log2FC, n=3).
I) Quantification graph of Msps intensity in qNSCs by normalizing against that in MB NSC at 0 h ALH (n=45 NSCs) and 6 h ALH (n=81 NSCs) in (H). ****p<0.0001.
Schematic outline of pΦ infection experiments. pΦ isolated from C57BL/6, phox-/-, IFNγ-/- mice were either left untreated or activated with IFNγ 12 h and LPS for the last 2 h prior to infection. Where indicated, NO inhibitor 1400W was added along with IFNγ. The intracellular bacterial viability was enumerated 96 hp.i.
E. OPA1-null mouse embryonic fibroblasts (MEFs) expressing control (empty vector) or OPA1 isoform 1 were cultured in normoxia or hypoxia (1% O2) for 24 hours. Cell lysates were analyzed by Western blotting with anti-OPA1 or anti-Tubulin antibody. Representative immunoblots were from n = 3 independent experiments.
E Western blot analyses of TFAM protein steady state levels in IMT1-resistant RKO cells in presence siRNAs against controls (control #1, #2) and TFAM (TFAM #1, TFAM #2) and treated with DMSO or IMT1. Images are representative of n=3 independent experiments. ACTINB is showed as loading control.
(C-E) Primary hippocampal neurons (DIV6+4) were transduced with lentivirus expressing shRNA targeting TDP-43 or a control. Immunoblots with the indicated antibodies (C). Quantification of VPS4B and TDP-43 protein level using densitometry (n = 4). Expression was normalized to the housekeeping gene β-actin (D).
with increasing doses of Nutlin 3a (i.e. 3.3 μM or 10 μM) using two independent probes. (D) Immunoblot analysis of samples treated N = 3 independent experiments.
G Cellular glucose uptake, lactate production, and oxygen consumption rates were measured in Dgcr8−/− ESCs stably expressing Mbd2 shRNAs.
(C) THP1 cells were infected with HSV-1 (KOS), HSV-2 (HG52), HSV-1 ΔICP27, or HSV-1 ΔICP27 rescued with HSV-2 ICP27 (MOI 3). Supernatants were harvested 18 hpi for measurement of type I IFN bioactivity.
E, F Efficacy of XMU-MP-5 in G1202R Ba/F3 xenograft mouse model. BALB/c nude mice bearing G1202R Ba/F3 cells xenograft tumors were administrated with vehicle or XMU-MP-5 by tail vein injection twice daily. Lorlatinib was used as a positive control by oral administration. Tumor volume (E) and tumor weight (F) were shown as mean ± SEM (n = 6). Statistical comparasions were performed using a two-tailed, unpaired Student's t test for (E), Vehicle vs XMU-MP-5 30 mg/kg, *P = 0.0433; Vehicle vs XMU-MP-5 30 mg/kg BID, **P = 0.0093; Vehicle vs Lorlatinib, **P = 0.0029. Statistical comparasions were performed using a one-way ANOVA with Dunnett test for (F). Vehicle vs XMU-MP-5 30 mg/kg, ***P = 0.0008; Vehicle vs XMU-MP-5 30 mg/kg BID, ***P = 0.0003; Vehicle vs Lorlatinib, ***P = 0.0002.
(H) WB analysis of tumor tissue lysates from two different mice with antibodies as indicated. L.E, Low exposure; H.E, High Exposure.
A Dose-response curves showing the effects of two independent anti-DDX3X siRNAs on the expression of AUG-NL-3xF (top) and (CGG)100 +1 NL-3xF (bottom) reporters. Plasmid-based reporters were transfected into HeLa cells 24 hours after knockdown, and reporter expression was quantified by luminescence. Nanoluciferase (NL) luminescence has been normalized to luminescence from firefly luciferase (FF), which was co-transfected, in order to control for transfection variability. Asterisks refer to comparisons between anti-DDX3X siRNAs and siRNAs against EGFP (siEGFP; two-way ANOVA with Dunnett's multiple comparisons test; n=12/condition). Data Information: For all panels, * P≤0.05, ** P≤0.01, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All panels depict data as means ± SD (compiled from ≥3 replicates).
(E) Volcano plot of differential super-enhancers targeting known leukemia and cancer genes. Examples include SE loss at CDKN1A, PI3KC2B and KMT2B (MLL2) and SE gain at FMOD, CREB3L2, CTLA4, TCF4, LEF1 and BCL2. Points represent non-differential SEs (grey), and differential SEs (FDR < 0.01) with fold change greater than 1 (orange).
Baseline associations between CSF T-tau, Ng and NFL and other AD traits. Data are estimates (-coefficients) from linear mixed effects models, with 95 % confidence intervals. The estimates are the main effects of the biomarkers, capturing the effects at study baseline. Effects were significant (*) for ADAS-cog: NFL in A-negative (p=.0013) and A-positive (p=.024). Biomarkers and outcomes were standardized to z-scores. Note that the y-axes for ADAS-cog are flipped, so that the lower ranges constantly reflect "worse" outcomes. Note also that the range of the y-axes differs for the different outcomes, for visualization purposes. Models were adjusted for age and sex, and education (for cognitive measures), and intracranial volume (for MRI measures). Aβ42 and T-tau were measured using the the INNOBIA AlzBio3 kit (Fujirebio, Ghent, Belgium), Ng was measured using an in-house immunoassay for Ng (Portelius et al, 2015) and NFL was measured using the NF-light® ELISA kit (Uman Diagnostics, Umeå, Sweden).
(a) p53 protein levels from mass-spectometry under oscillatory dynamics were used to fit the production and degradation rates (kpmRNA and kdmRNA, respectively) for MDM2 mRNA. The MDM2 mRNA levels (from RNA-seq data in Fig 1) were used to fit the production and degradation rates (kpprot and kdprot, respectively) for MDM2 protein. The experimentally observed and fitted measurements are shown, along with the R2 value of the correlation between the two.
d, Thioester formation between Apg8 and Apg7. Cell extracts of Δapg7Δapg8 cells expressing Apg7-Myc and/or HA-Apg8 from 2µ plasmids were immunoprecipitated with anti-HA antibody, and immunoblotted (IB) with anti-Myc and anti-HA antibody. DTT-, no DTT; DTT+, 100 mM DTT; asterisk, Apg8-Apg7 conjugate.
H Schematic of trafficking assay. Surface EGFR is labelled and internalized at 16°C or recycled at 37°C. Acid washing removes labelled surface pools and allows analysis of the internal pool of EGFR originating from the surface.
(B) The cytosolic (Cyto) and mitochondrial (Mito) fractions were isolated from HepAD38 cells grown in the absence or presence of tetracycline for 48 h. Cellular fractions were analyzed by Western blotting with antibodies specific for the indicated proteins. Fractions: WCL, whole cell lysates; Cyto, purified cytoplasm; Mito, purified mitochondria. Organelle markers: VDAC1, mitochondria; GAPDH, cytoplasm.
Mice lungs were collected from PBS-(mock) vaccinated BALB/c mice at day 5 post-RSV infection, fixed, paraffin embedded, and slides were processed for imaging. Immunohistochemistry staining of lung sections shows RSV protein localized to distal alveoli by Control rabbit sera (left panels) or rabbit anti-sera against RSV F protein (center panels), or against RSV F-p27 (110-136) peptide (right panels). Scale bar = 100 µm. The percentage of cells positive for RSV-F (middle panel) and RSV-p27 (right panel) covering 500 x 500 µm of lung tissue for each mice for each antibody staining are shown. The experiments were performed twice and variation between the two independent expeiremnts was <9%.
MMTV-PyMT mice were injected with CIP2A-BP or svCIP2A-BP via mammary fat pad. Macroscopic and histological analysis of the lungs of 140 days old MMTV-PyMT mice; lung metastatic nodules were visualized 8 weeks post-transplantation (5 mice per group). Right panel is the quantification of pulmonary metastases.
(h) ChIP analysis from liver of mice fed ad libitum or 24 h fasted. The CLEAR elements in the first intron of Tcfeb genomic DNA are shown as numbered black rectangles as indicated in Supplementary Table S1. Red rectangles represent exons, and the ATG indicates the first codon (from the mouse Tcfeb isoform b). The histogram shows the amount of immunoprecipitated DNA as detected by quantitative PCR assay. Values were normalized to the input and plotted as relative enrichment over a mock control. Data represent mean ± s.d of 3 independent experiments.
Confocal analysis of co-localization of CFP-NbATG8f-labelled autophagic bodies with the VISP1-YN and SGS3-YC bodies in N. benthamiana leaves. The infiltrated leaves were treated with 100 µM E64d or DMSO at 48 hpi and examined for imaging at 60 hpi. Scale bar = 20 μm.
Heatmaps of total RNA read density ratios between untreated (control) and α‐amanitin‐ or ML‐60218‐treated HeLa cells.
(A) Experimental scheme for contextual fear conditioning, Barnes maze, and novel object recognition tests with intraperitoneal injections of TAT or TAT-pS3 peptide (2 mg/kg) in Nedd4-2 WT or Nedd4-2 cKO mice at 6-8 weeks of age.
F, G Frequencies of human lymphoma cells, as judged by hCD45 expression, among all (human and mouse, h+m) CD45+ leukocytes in the spleen (S), femoral bone marrow (BM) and jaw bone marrow (JB) at the study endpoint of the mice shown in D (four weeks post injection for U-2932, five weeks p.i. for RIVA and six weeks p.i. for RC-K8).