EMBO/sd-character-level-ner huggingface dataset:
Figure 1Schematic showing the OptoCAR replacing the antigen receptor (dotted region) as the primary driver of intracellular T cell signaling. Illumination of the cells leads to the dissociation of the intracellular signaling domain of the OptoCAR complex and the loss of signal transduction. The network nodes investigated in this study are explicitly depicted within the boxes. A more detailed schematic of the bipartite OptoCAR complex from (A) with component parts labelled. Light-mediated disruption causes dissociation of intracellular signaling tail (ζ‑chain) from the extracellular binding domain. OptoCAR-T cell engagement with an antigen-presenting cell (APC) does not initiate signaling in the absence of the dimerizer small-molecule. OptoCAR signaling from within these cell conjugates is modulated by transitioning from the dark (signaling competent) state to the 'Off' state by illuminating cells with blue light. The intracellular domain will be rapidly dephosphorylated when it diffuses away from the bound OptoCAR. Stills from Movie EV1 showing the membrane-bound form of the OptoCAR expressed in HEK293T cells being reversibly dissociated from the extracellular domain by single-cell illumination (blue box). The intracellular part of the OptoCAR used in this experiment was not myristoylated so it localized to the cytoplasm on dissociation, to aid visualization of OptoCAR dynamics. Scale bar: 5μm. Quantification of the light-mediated dissociation of OptoCAR in HEK293T cells by measuring the ratio of membrane-bound intracellular part of OptoCAR over time. Individual cells were illuminated after 25 seconds of imaging for 25 seconds to calculate dissociation rate (green) before returning to dark (signaling competent) state to calculate re-association rate (red line). A unitary value was assigned to the mean membrane fluorescence prior to illumination and zero to the minimum value. Raw plots are presented in Appendix Fig S1. Bounding area around datapoints shows mean ± SEM (n=12 cells).
Identification of the cluster specific molecular pathways and of the filiation between the NI clusters.Figure 4A) Heatmap representing the z-score for the top 5 regulons of each cluster determined with SCENIC. The dendrogram on the left side of the panel indicates the correlation between the regulons across the dataset. The z-score is indicated with a gradient from magenta (z-score < 0, the regulon is repressed) to yellow (z-score > 0, the regulon is active). B) Dendrogram representing the distance among the clusters. The tree was built on the correlation (Spearman) calculated on the regulon matrix from the NI dataset. C) Lineage prediction using RNA Velocity. The arrows and lines on the UMAP predict the "direction" taken by the cells of each cluster, based on the comparison between the levels of mRNA and pre-mRNA. Note that the clusters CC and PL-ImpL2 (dashed lines) have been moved from their original position to fit in the graph. D) Single cell trajectory reconstructed with monocle 2 on the NI dataset. The first panel shows the overlap of all clusters and subsequent panels show restricted number of clusters for which the RNA velocity analysis suggested a filiation.
Lamplight causes sustained reversible hyperpolarisation in SCN neuronsA) Schematic of Lamplight AAV delivery to the suprachiasmatic nucleus (SCN) of VIPCre/+ mice.Figure 2A) Schematic of Lamplight AAV delivery to the suprachiasmatic nucleus (SCN) of VIPCre/+ mice. Whole cell patching of SCN slices (bottom left) made by targeting mCherry fluorescent neurons (arrows, bottom right) B) Representative trace of hyperpolarisation to 405nm light in a Lamplight-expressing SCN neuronD) Representative trace showing hyperpolarisation was sustained during dark after 405nm light (5s) and reversed by 525nm light (15s) E) Hyperpolarisation and depolarisation of a Lamplight-expressing neuron by 405nm and 525nm light, respectively, across multiple stimulus presentations F) Three example traces from a single cell exposed to 405nm followed by 525nm light. Individual traces were fit with exponential decay (405nm, blue) or association curves (525nm, green) for 6 trials across 2 cells G, H) Parameters from best-fit curves used to calculate (G) latency (ms) and (H) half-life (ms).  I) Simultaneous 525nm and 405nm light prevents spike silencing J) Constant 405nm light (12.9 log photons) presented with 525nm light of decreasing intensity from 14.9 - 12.9log photons in 6 steps of 10s (left) or 20s (right). 525nm light antagonised the 405nm-driven hyperpolarisation for all intensities except 12.9log photons
Figure 4(A) A partial protein alignment of select IFITM3 genes from various primate species for which a reference genome is available and accessible in Genomicus. Sequences from the Mouse Lemur and Colobus monkey were identified by BLAST analysis of reference genomes in NCBI GenBank. Gene location is indicated, when available, by chromosome number and an asterisk indicates that the given gene sequence falls into a canonical IFITM locus with flanking B4GALNT4 and ATHL1 genes. The suborder and parvorder (from left to right) indicate taxonomical relationships between species. Residues bolded in red highlight non-synonymous substitutions that disrupt canonical motifs for the recruitment of NEDD4 and AP-2. A complete protein alignment of all IFITM sequences analyzed in this study is availble in the Appendix. (B) A phylogenetic gene tree (cladogram) indicates the relationship among IFITM3 sequences analyzed in this study. The final consensus tree was made by merging results from neighbor joining and maximum likelihood phylogenetic reconstructions using both nucleotide and amino acid sequences in Ensembl (see Figure EV4 for robustness measurement by Bayesian inference). Branch lengths are normalized and arbitrary. The size of triangles at the tree tips roughly correspond to the number of sequences contained therein. Note that the IFITM2 gene is the most recent member of the IFITM locus, appearing only in human, chimpanzee, and gorilla genomes. (C) A graphical representation of naturally occurring truncated forms of IFITM3 identified in the vervet and marmoset reference genomes, as compared to the putative Δ1-21 variant in humans.
Figure 6A) Structural presentation of CrossMAb RG7716 with substituted amino acids highlighted and colored. Amino acids corresponding to individual point mutations ensuring correct and efficient heavy chain heterodimerization ('knobs-into-holes' [green] and additional disulfide bridge [yellow]), abolishing Fc-receptor functionality (Fc-gamma receptors I, II, and III, colored in pink) and Fc-Rn (colored in blue) are highlighted. B) Summary table of experimental binding affinities of the parental components targeting VEGF-A (ranibizumab) and ANG-2 (LC10) as well as of RG7716 measured by isothermal titration calorimetry. RG7716 binds VEGF-A121 and -165 with an affinity comparable to ranibizumab (3.3 vs. 3.1 nM). ANG-2 binding of RG7716 is slightly decreased to 22 nM compared to α-ANG-2 IgG1 (LC10) with 4.1 nM. No binding to ANG-1 was detectable for RG7716 or α-ANG-2 IgG1 (LC10). C) Inhibition of ANG-1 induced endothelial cellsurvival was tested in the presence of increasing concentrations of LC10 (anti-ANG-2IgG, ANG-2 binding part in RG7716) and LC08 (ANG-1 and ANG-2 binding antibody). An average of three independent experiments is shown with SEM. D) The ability of RG7716 to bind to ANG-2 and VEGF-A simultaneously and independent is demonstrated by a surface plasmon resonance experiment. RG7716 is captured via an anti-Fc antibody on the chip surface. The green curve depicts the experiment with ANG-2 in the first and VEGF-A in the second binding event. The red curve shows the binding events in the other sequence.
Figure 1A. Binding regions of the 10B3 antibody as determined by conjugation mass spectrometry (in dark red) and of J591 (in yellow) Bander et al, 2003a() are labeled in a 3D model of the PSMA-molecule as reported by Davis et al. Davis et al, 2005() in a dimeric (left panel) or monomeric (right panel) representation of the molecule (PDB ID code 1Z8L). Apical, helical and protease domains are colored in green, grey and blue respectively. B, C. Cryosections of samples from patients with prostate carcinoma and SCC of the lung. Samples were processed as described in the methods section. Ve=vessel, Tu=tumor. Scale 50µm. See also Fig 1D for comparative semi-quantitative analysis of a panel of samples from patients with prostate carcinoma, lung SCC and non-lung SCC. D. Semi quantitative analysis of binding of the PSMA antibodies 10B3 and J591 to cryosections from different tumor entities. For definition of the H-score reflecting binding intensity, refer to the methods section. Statistical analysis was performed using the paired, non-parametric Wilcoxon test. Sample size (n) and the corresponding P-values are indicated in the graphs.
Figure 2(A) A northern blot depicting a time course experiment ranging from five minutes to 24 hours of MCF10A cells in response to oxidative stress. A single probe complementary to pre-tRNATyrGUA, mature tRNATyrGUA, and tRFTyrGUA expression was 32P-labeled and used for detection. (B) Quantification of pre-tRNATyrGUA (left) and mature tRNATyrGUA levels (right) by northern blot analysis from multiple independent experiments (normalized to U6 levels) are shown (n=6). (C) MCF10A cells were exposed to oxidative stress (200μM H2O2) once daily for five continuous days. (D) Quantification of mature tRNATyrGUA bands by northern blot after cells were treated once daily for five continuous days (normalized to U6) from multiple independent experiments (n=12). (E) Quantification of northern blot analysis for pre-tRNATyrGUA (left) and tRNATyrGUA (right) after one hour and 24 hours respectively in HBEC30 cells upon exposure to oxidative stress (200μM H2O2) as in (A) (n=6).
Figure 5Representative movie montage of a live-cell imaging experiment illustrating the dynamics of CHMP4B-eGFP and mCherry-Galectin3 recruitment at different time points before and after LLOMe treatment. Using the perfusion system, 250 μM LLOMe was added to HeLa cells stably expressing CHMP4B-eGFP and mCherry-Galectin3 and images were acquired every 20 sec for a period of 20 min. As shown in the representative movie montage and the quantification graph, CHMP4B recruitment precedes Galectin3, which is an established marker for detection of damaged endolysosomal membranes. The quantification graph is normalized to the area occupied by the cells. Data were obtained from >40 cells per condition from three independent experiments. Error bars correspond to 95% confidence intervals. Data information: Scale bars: 5 μm.
BRC-1/BRD-1-dependent and -independent germline responses to mitochondrial-stress.Figure 6A Quantification of BRD-1 protein and representative western blot from wild-type worms fed bacteria transformed with either empty-vector (con) or with vector expressing dsRNA against frh-1 or isp-1 Bar graphs are mean ± SEM Data information: Data are presented as mean ± SD N= 8-1 worms per replicate and condition, * P < 0.05, *** P < 0.001 and **** P < 0.0001 vs untreated; ### P<0.001 and #### P < 0.0001 vs con. Not significant if nothing is specified B Quantification of mitotic nuclei in single gonad arm of wild-type (WT), brc-1(tm1145) and brd-1(gk297) strains fed as in (A) Data information: Data are presented as mean ± SD N= ), 8-1 worms per replicate and condition, * P < 0.05, *** P < 0.001 and **** P < 0.0001 vs untreated; ### P<0.001 and #### P < 0.0001 vs con. Not significant if nothing is specified Quantification of apoptotic corpse in wild-type (WT), brc-1(tm1145) and brd-1(gk297) strains fed as in (A) and left untreated (C Bar graphs are mean ± SEM. Data information Data are presented a mean ± SEM N= 8-10 worms per replicate and condition, * P < 0.05, *** P < 0.001 and **** P < 0.0001 vs untreated; ### P<0.001 and #### P < 0.0001 vs con. Not significant if nothing is specified. 2-way ANOVA Tukey"s multiple comparison Quantification of apoptotic corpse in wild-type (WT), brc-1(tm1145) and brd-1(gk297) strains fed as in (A) an treated with ionizing radiation 125 Gy (IR) (D). Bar graphs are mean ± SEM. Data information: Data are presented a mean ± SEM N= 8-10 worms per replicate and condition, * P < 0.05, *** P < 0.001 and **** P < 0.0001 vs untreated; ### P<0.001 and #### P < 0.0001 vs con. Not significant if nothing is specified. 2-way ANOVA Tukey"s multiple comparison
Figure 2Percentages of axons that initiated regeneration 24 h after laser surgery. The numbers (n) of animals examined are shown. Error bars indicate 95% CI. Data information: In (A), statistical significance was determined by Fisher's exact test; ***P <0.001; NS; not significant. B Induction of Psvh-2::nls::venus expression in D-type motor neurons by laser surgery. Expression of fluorescent proteins in D-type motor neurons of wild-type, mxl-1, tdpt-1 and mxl-1; tdpt-1 animals 3 h after laser surgery are shown. Yellow arrowheads and white arrows indicate axon and cell bodies, respectively, of D-type neurons. White arrows indicate the sites of laser surgery. D neurons are visualized by CFP under control of the unc-25 promoter. Cell bodies of D-type neurons are magnified and shown within the red boxes. Most of the intestinal fluorescence in these photos is from endogenous and variable background autofluorescence. A schematic representation of D-type motor neurons is shown on the bottom. Scale bars = 10 μm.
Human Aβ exhibits a biphasic profile in CSF of APP transgenic mice.Figure 1Human Aβ exhibits a biphasic profile in CSF of APP transgenic miceA, B Aβ40 and Aβ42 concentrations in CSF of male APP23 mice (heterozygous; 3 (n = 14), 6 (n = 12), 8 (n = 10), 12 (n = 11), 19 (n = 9), and 25 (n = 6) months of age). CSF Aβ40 (F(1, 56) = 22.351, P < 0.001) as well as CSFAβ42 (F(1, 56) = 38.597, P < 0.001) followed a significant quadratic trend. C Aβ42/40 ratio in CSF of APP23 mice showed a delayed decrease with age (F(1, 56) = 53.894, P < 0.001). D, E Aβ40 and Aβ42 concentrations in CSF of male and female APP24 mice (homozygous; 2 (n = 13), 3-4 (n = 16), 7-8 (n = 15), 18-19 (n = 14), 24 (n = 16), and 30 (n = 18) months of age). CSF Aβ40 followed a significant quadratic trend (F(1, 86) = 6.678, P = 0.011) and CSF Aβ42 best fitted a cubic trend (F(1, 86) = 30.599, P < 0.001). F Aβ42/40 ratio in CSF of APP24 mice showed a delayed decrease with age (F(1, 86) = 64.936, P < 0.001). G, H Aβ40 and Aβ42 in the CSF of female APP51 mice (heterozygous; 3 (n = 6), 15 (n = 8), and 24 (n = 8) months of age; 22 mice in total). CSF Aβ40 (F(1, 19) = 37.349, P < 0.001) as well as CSFAβ42 (F(1, 19) = 107.670, P < 0.001) followed a significant quadratic trend. I Aβ42/40 ratio in CSF of APP51 mice showed a delayed decrease with age (F(1, 19) = 26.367, P < 0.001).
a, &agr-KG extends the lifespan of adult worms in the metabolite longevity screen.f1a, alpha-KG extends the lifespan of adult worms in the metabolite longevity screen. All metabolites were given at a concentration of 8 mM. b, Structure of α-KG. c, Dose-response curve of the α-KG effect on longevity. d, e, α-KG extends the lifespan of worms fed bacteria that have been ampicillin arrested, mean lifespan (days of adulthood) with vehicle treatment (mveh) = 19.4 (n = 80 animals tested), mα-KG = 25.1 (n = 91), P  0.0001 (log-rank test) (d); or γ-irradiation-killed, mveh = 19.0 (n = 88), mα-KG = 23.0 (n = 46), P  0.0001 (log-rank test) (e). OP50, E. coli OP50 strain. f alpha-KG does not further extend the lifespan of ogdh-1 RNAi worms, mveh = 21.2 (n = 98), mα-KG = 21.1 (n = 100), P = 0.65 (log-rank test).
Figure 6Representative pictures showing the influence of mouse Rspondin type and concentration on growth of replated Lgr5-DTReGFP WT and Lgr5 KO organoids after 4 days of culture. Arrows show alive elements and arrow heads dead elements. Organoid morphology depends on Rspondin ligand type and concentration. Left panel: growth quantified as the percentage of elements present at day1 surviving at day4. A mean of 100 elements were analyzed per sample and per condition (n: 4 WT, 2 KO organoid culture samples, each originating from a given embryo). Right panel: organoid complexity measured by branching coefficient. Each symbol indicates the value of a given organoid (analysis was done on 4 WT and 2 KO organoid culture samples, each originating from a given embryo). Heatmap showing the impact of Rspondin type and concentration (ng/ml) on relative Wnt target gene expression (list from the Sansom APC data set) in Lgr5-DTReGFP WT and KO organoids analyzed by RNAseq (n= 3 WT and 2 organoid culture samples, each originating from a given embryo). Gene expression analysis by qRT-PCR of stem cell markers in Lgr5-DTREeGFP WT and KO organoids after 5 days of culture (expression relative to reference genes). Each symbol indicates the value for an organoid culture originated from a given embryo. Immunofluorescence showing Olfm4+ve cells in Lgr5-DTReGFP WT and KO organoids cultured in Rspo2 conditions. Epithelium is delineated with b-catenin and nuclei counterstained with DAPI (Merge). Insets: white arrowheads evidence Olfm4+ve cells concentrated in organoid protrusions. Quantification of Olfm4+ve area with respect to the total epithelial area. Each symbol indicates the value for an organoid culture originating from a given embryo.
Tpl2[D270A] mutation impairs macrophage killing of S.Figure 6A. BMDMs of the indicated genotypes were infected with YFP-S. aureus (MOI 10) for 0.5h. S. aureus CFU were assessed at 8 h after infection and normalised to CFU at 1 h (n = 12; 2 biological and 6 technical replicates per condition per experiment). As a control, WT cells were treated with bafilomycin A to block V-ATPase acidification of phagosomes and phagosome proteolysis. Data information: One representative experiment out of three shown. Error bars represent SEM. ** P < 0.01, *** P < 0.001, **** P < 0.0001, not significant (ns). one-way ANOVA.  B. Quantification of YFP-S. aureus average fluorescence intensity per cell from Figure 5 panel (A) (n = 66-85 cells). Data information: One representative experiment out of three shown. Error bars represent SEM. ** P < 0.01, *** P < 0.001, **** P < 0.0001, not significant (ns). one-way ANOVA.  C. Cell death following was assayed by measuring LDH release from cytosol of BMDMs 8h and 24h post-infection with S. aureus (MOI 10; n = 4 wells). Data information: One representative experiment out of three shown. Error bars represent SEM. ** P < 0.01, *** P < 0.001, **** P < 0.0001, not significant (ns). one-way ANOVA.  D. Whole cell extracts from WT and Tpl2[D270A] BMDMs following S. aureus infection (MOI 10) were immunoblotted for the gasdermin D p30 cleavage product. HSP90 was used as a loading control. Data information: One representative experiment out of three shown. Error bars represent SEM. ** P < 0.01, *** P < 0.001, **** P < 0.0001, not significant (ns). one-way ANOVA.  E. BMDMs of the indicated genotypes were infected with GFP-C. rodentium (MOI 2) for 0.5h. C. rodentium CFU were assessed at 2 h after infection and normalised to CFU at 0.5 h (n = 12; 2 biological and 6 technical replicates per condition per experiment). As a control, WT cells were treated with bafilomycin A. Data information: One representative experiment out of three shown. Error bars represent SEM. ** P < 0.01, *** P < 0.001, **** P < 0.0001, not significant (ns). one-way ANOVA.  F. Representative images of GFP+ BMDMs labelled with LysoTracker Red DND-99 dye (red) and DAPI, 1h post-infection with GFP-C. rodentium (green). G. Quantification of LysoTracker Red co-localisation with GFP- C. rodentium from panel (F) (n = 54-63 cells). Data information: One representative experiment out of three shown. Error bars represent SEM. ** P < 0.01, *** P < 0.001, **** P < 0.0001, not significant (ns). P one-way ANOVA.
Hyperactivation of microglia in Grn-/- mice is not deleteriousA.Figure 9A. Immunoassay-based quantification of neurofilament-light chain (NfL) protein levels in CSF of 6-month-old Grn-/- (n=4), Trem2-/-(n=4), Double-/- (n=4) and WT (n=5) male mice. B. Immunoassay-based quantification of NfL levels in CSF of 14-month-old Grn-/-, Trem2-/-, Double-/- and WT female mice (n=3 per genotype). Data information: Data in A, B represent mean ± SEM. For statistical analysis in A-B two-way ANOVA with Dunnett`s post hoc test was used the unpaired C. Neuropathology NanoString panel analysis of total brain mRNA expression of 6-month-old and 14-month-old Grn-/-, Trem2-/-, Double-/- and WT male mice based on NanoString advanced analysis R-script included in the panel (6-month-old mice: n=4, 14-month-old mice: n=3). D. Transcript levels of all significantly changed genes in Double-/- vs. Grn-/- brain mRNA of 6-month-old and 14-month-old mice analyzed in C. Grin3b was under detection limit in the 14-month-old cohort. Transcript expression is normalized to the mean of the WT cohort. Data in D represent mean ± SEM. in D two-tailed student`s t-test was performed. E. The same cohort of mice scanned for TSPO-PET were additionally scanned for FDG-PET. Axial slices as indicated show %-FDG-PET differences between Grn-/-, Trem2-/- and Double-/- (all cold colour scales) when compared to WT at the group level. Images were adjusted to an MRI template. F. Bar graph illustrates individual FDG-PET values derived from a whole brain volume of interest. Data represent mean ± SD. 8-15 female mice per group at an average age of 10.7 ± 1.5 months (Grn-/- n = 8, Trem2-/- n = 10, Double-/- n = 10, WT n = 15) were used. Data in F two-tailed student`s t-test was performed.
Figure 4A. Representative contrast-enhanced MRI panels depicting the liver of Mock/Tie2-GFP (red frame) or Tie2-IFNα (blue frame) chimeric mice. Each frame shows the metastatic progression 14 and 21 days post-intrasplenic injection of 5x104 MC38 within the indicated chimeric group. BM donors and recipient mouse strains are indicated on the left of each frame; red arrows or dashed red lines identify CRC liver metastases of representative z-sections. Tumors were identified as hypointense and slightly-hyperintense regions in T1 and T2 weighted sequences respectively; scale bars=5mm.B. Tumor volume quantification (based on MRI analyses) of lesions detected in the same livers described in A. Chimeric groups and number of mice analyzed are listed; data pooled from three independent experiments; mean values are shown; error bars=S.E.M.; p-values were calculated by Mann-Whitney test.