10,653 research outputs found
Response to TGFβ1 correlates with nuclear levels of YAP.
No full text(A-F) NHDF, NHCF and NHLF were starved and then treated with 5ng/ml TGFβ1 alone or in combination with indicated YAP modulators; concentration-response curve (CRC) of LPA and S1P (10-fold dilutions starting at 1μM), thrombin (10-fold dilutions starting at 1mU/ml), 500nM latrunculin B (lat B), 2ng/ml Rho inhibitor (inh), 10μM forskolin, 50mM 2-DG or 1ng/ml Rho activator (act). Integrated nuclear intensity of YAP was analysed after 1h by high content imaging analysis of cells stained against YAP and expressed as fold change (FC) versus TGFβ1-only treated cells. The same treatments were done for 3h to measure gene expression by RT-qPCR and for 24h to analyse PAI-1 in cell supernatants by ELISA. PAI-1 levels and gene expression were correlated (linear correlation) with YAP nuclear staining. (n = 3–4; YAP imaging). (n = 3; RT-qPCR). (n = 4–8; ELISA). Mean+/- SEM.</p
Metadata Representations for Queryable ML Model Zoos
No full textMachine learning (ML) practitioners and organizations are building model zoos of pre-trained models, containing metadata describing properties of the ML models and datasets that are useful for reporting, auditing, reproducibility, and interpretability purposes. The metatada is currently not standardised; its expressivity is limited; and there is no interoperable way to store and query it. Consequently, model search, reuse, comparison, and composition are hindered. In this paper, we advocate for standardized ML model metadata representation and management, proposing a toolkit supported to help practitioners manage and query that metadata.Web Information SystemsHuman-Centred Artificial Intelligenc
A Manifesto of Nodalism
Full text linkThis paper proposes the notion of Nodalism as a means describing contemporary culture and of understanding my own creative practice in electronic music composition. It draws on theories and ideas from Kirby, Bauman, Bourriaud, Deleuze, Guatarri, and Gochenour, to demonstrate how networks of ideas or connectionist neural models of cognitive behaviour can be used to contextualize, understand and become a creative tool for the creation of contemporary electronic music
GPCR ligands activate YAP to enhance TGFβ1 response.
No full text(A) NHDF were starved and stimulated with 1μM LPA, 1μM S1P or 1mU/ml thrombin for 1h and the whole cell lysates were analyzed by western blot for pS127 YAP, YAP and GAPDH. Representative images are shown. The western blots were quantified by image densitometry. The pYAP signal was normalized to total YAP and expressed as fold change relative to vehicle-treated samples (n = 4–6, biological replicates). Mean+/- SEM. One-sample t-test against the normalized value 1 (vehicle) was performed. (B) NHDF were treated as in A and the level of YAP was determined in nuclear fractions. Representative images are shown. The western blots were quantified by image densitometry. The YAP signal was expressed as fold change relative to vehicle-treated samples (n = 3–4, biological replicates). Mean+/- SEM. cJUN was used as a control for nuclear fraction. One-sample t-test against the normalized value 1 (vehicle) was performed. (C) NHDF were treated as in A. The nuclear intensity of YAP was analyzed by high content imaging of cells stained with anti-YAP antibody. Results were normalized to vehicle-treated cells. Example images are shown on the right (n = 3–4). Mean+/- SEM. One sample t-test was performed comparing normalized treatment effects to value 1 (vehicle). (D) NHDF were starved and stimulated for 1h with 1μM LPA, 1μM S1P or 1mU/ml thrombin with or without 5ng/ml TGFβ1. The interaction between nuclear YAP and Smad2 was monitored by proximity ligation assay. Results were normalized to vehicle-treated cells. FC—fold change (n = 4). Mean+/- SEM. Statistics are summarized in S6 Table. (E) NHDF were starved and stimulated for 24h with an increasing concentration of TGFβ1 alone or in combination with 1μM LPA, 1μM S1P or 1mU/ml thrombin. PAI-1 in cell supernatant was determined by ELISA (n = 3). Mean+/- SEM. (F-H) NHDF were starved and stimulated for 3h as in G. CTGF, EDN1 and CYR61 expression was determined by RT-qPCR (n = 3). Mean+/- SEM.</p
Expanding the Hippo pathway : hMOB3 modulates apoptotic MST1 signaling and supports tumor growth in glioblastoma
Full text linkProtein kinases are critical players of signal transduction pathways involved in development, physiological and pathological processes. Deregulation of protein kinase signaling is found to be causal or related to varieties of human diseases, such as cancer, cardiovascular disease and diabetes. The human genome encodes 518 protein kinases. Approximately 60 out of them belong to the AGC group of Serine/Threonine protein kinases, including the ste20 like MST kinase family and NDR kinase family. Members of these families are highly conserved from yeast to men and regulate essential processes such as growth, proliferation and apoptosis. The Hippo pathway is a recently identified tumor suppressive network, where the MST-NDR family kinases form a kinase cascade regulating the downstream signaling through the effector YAP/TAZ.
In addition to signaling through the NDR family kinases, the Hippo/MST kinases also control cell apoptosis bypass these classical effectors YAP/TAZ. Despite the fact that JNK, FOXO3, H2B are well characterized downstream targets of apoptotic MST kinases, the regulatory mechanisms of apoptotic MST signaling are still largely unknown.
The human MOB family consists of six members encoded by six different genes (hMOB1A, -1B, -2, -3A, -3B and -3C). While as an activator for hMOB1A/B in MST-LATS/NDR kinase cascade, hMOB2 is a specific negative regulator of NDR kinase by competing the binding of hMOB1 to NDR kinase. Although hMOB3 family members share higher amino acid identity with hMOB1 than hMOB2, hMOB3 proteins do not interact or (de)activate NDR family kinases. Hence, the functions of hMOB3A/B/C are completely undefined.
A previous microarray study performed in the lab indicated that hMOB3 family members were deregulated in glioblastoma. In the present study, we first investigated the pathological roles of human MOB3 proteins and found that hMOB3 is highly upregulated in glioblastoma. Moreover, mRNA expression levels of hMOB3 members correlate with survival, suggesting hMOB3 members as potential prognostic markers. We extended the biochemical analysis by looking for the interaction partners of hMOB3 and demonstrated that hMOB3 binds to MST1 and inhibits the apoptotic cleavage of MST1 kinase. We further verified that hMOB3 promotes tumorigenesis of gliobalstoma cells in vivo by a U87MG derived flank model. Taken together, our results suggest that manipulate hMOB3 might represent a therapeutic strategy in malignant gliomas
Optimizing ML Inference Queries Under Constraints
No full textThe proliferation of pre-trained ML models in public Web-based model zoos facilitates the engineering of ML pipelines to address complex inference queries over datasets and streams of unstructured content. Constructing optimal plan for a query is hard, especially when constraints (e.g. accuracy or execution time) must be taken into consideration, and the complexity of the inference query increases. To address this issue, we propose a method for optimizing ML inference queries that selects the most suitable ML models to use, as well as the order in which those models are executed. We formally define the constraint-based ML inference query optimization problem, formulate it as a Mixed Integer Programming (MIP) problem, and develop an optimizer that maximizes accuracy given constraints. This optimizer is capable of navigating a large search space to identify optimal query plans on various model zoos.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Web Information SystemsHuman-Centred Artificial Intelligenc
GPCR ligands regulate TGFβ1 response via the Rho/YAP axis.
No full text(A) Human dermal fibroblasts were starved and stimulated with 5ng/ml TGFβ1, 1ng/ml of Rho activator (Rho Act) or a combination of the two. PAI-1 levels in the cell supernatant were measured by ELISA after 24h (n = 9). Mean+/- SEM. (B) CTGF, EDN1 and CYR61 expression was measured by RT-qPCR after 3h in NHDF treated as indicated (n = 3). Mean+/- SEM. (C) αSMA levels were determined by western blot at 24h in cells treated as in A. The signal for αSMA was measured by image densitometry and expressed as relative value compared to vehicle-treated sample (n = 2). Mean+/- SEM. (D) NHDF were starved and stimulated with 5ng/ml TGFβ1, 1ng/ml of Rho activator (Rho Act) or a combination of the two for 1h. The nuclear intensity of YAP was analyzed by high content imaging of cells stained with anti-YAP antibody. Results were normalized to vehicle-treated cells (n = 4). Mean+/- SEM. One sample t-test was performed comparing normalized treatment effects to value 1 (vehicle). (E, F) NHDFs were starved, pretreated with Rho inhibitor (2ng/ml) and stimulated with 5ng/ml TGFβ1, 1μM LPA or the combination. PAI-1 levels in the cell supernatant were measured by ELISA after 24h (n = 6). Mean+/- SEM. αSMA levels were determined by western blot at 24h. The signal for αSMA was measured by image densitometry and expressed as relative value compared to vehicle-treated sample (n = 2). Mean+/- SEM. (G) NHDFs were starved, pretreated with Rho inhibitor (2ng/ml) and stimulated with 5ng/ml TGFβ1, 1μM LPA or the combination for 1h. The nuclear intensity of YAP was analyzed by high content imaging of cells stained with anti-YAP antibody. Results were normalized to vehicle-treated cells (n = 3). Mean+/- SEM. One sample t-test was performed comparing normalized treatment effects to value 1 (vehicle). (H) NHDF were transfected with myc-YAP WT or myc-YAP5SA and stimulated with 5ng/ml TGFβ1 or vehicle. PAI-1 levels in the cell supernatant were measured by ELISA after 24h (n = 12). Mean+/- SEM.</p
Alteration in branching morphogenesis via YAP/TAZ in fibroblasts of fetal lungs in an LPS-induced inflammation model
No full textAbstract Background Chorioamnionitis is a common cause of preterm birth and leads to serious complications in newborns. The objective of this study was to investigate the role of the Hippo signaling pathway in lung branching morphogenesis under a lipopolysaccharide (LPS)-induced inflammation model. Materials and methods IMR-90 cells and ex vivo fetal lungs were treated with 0, 10, 30, or 50 μg/ml LPS for 24 and 72 h. Supernatant levels of lactate dehydrogenase (LDH), interleukin (IL)-6, IL-8, Chemokine (C-X-C motif) ligand 1(CXCL1), branching and the surface area ratio, Yes-associated protein (YAP), transcription coactivator with PDZ-binding motif (TAZ), fibroblast growth factor 10 (FGF10), fibroblast growth factor receptor II (FGFR2), SRY-box transcription factor 2 (SOX2), SOX9, and sirtuin 1 (SIRT1) levels were examined. Differentially expressed genes in fetal lungs after LPS treatment were identified by RNA-sequencing. Results LPS at 50 μg/ml increased IL-6 and IL-8 in IMR-90 cells and increased IL-6, CXCL1 and LDH in fetal lungs. The branching ratio significantly increased by LPS at 30 μg/ml compared to the control but the increased level had decreased by 50 μg/ml LPS exposure. Exposure to 50 μg/ml LPS increased phosphorylated (p)-YAP, p-YAP/YAP, and p-TAZ/TAZ in IMR-90 cells, whereas 50 μg/ml LPS decreased FGF10 and SOX2. Consistently, p-YAP/YAP and p-TAZ/TAZ were increased in fibronectin+ cells of fetal lungs. Moreover, results of RNA-sequencing in fetal lungs showed that SMAD, FGF, IκB phosphorylation, tissue remodeling and homeostasis was involved in branching morphogenesis following exposure to 50 μg/ml LPS. The p-SIRT1/SIRT1 ratio increased in IMR-90 cells by LPS treatment. Conclusions This study showed that regulation of the Hippo pathway in fibroblasts of fetal lungs was involved in branching morphogenesis under an inflammatory disease such as chorioamnionitis
The role of YAP in regulating apoptosis in the developing sea urchin
No full textHippo signaling pathway regulates tissue and organ development by controlling Yes-associated protein (YAP), a co-transcriptional regulator that activates anti-apoptosis and pro-cell proliferation genes in the nucleus. Hippo pathway components have been identified in sea urchin genome, but no functional characterization has been published. Our lab showed YAP specific inhibitor, verteporfin, reduced cell numbers per embryo at the early and late gastrula stage, suggesting YAP controls embryonic growth. Verteporfin inhibition of YAP resulted in a concentration-dependent increase in apoptosis, with highest apoptotic cell numbers per embryo at 48 hours with 10 ug/mL verteporfin. Apoptotic cells were detected at 48 hours in treated embryos in all three germ layers, suggesting apoptosis from YAP inhibition is not germ layer specific. We are now analyzing apoptosis using Western blot analysis to detect PARP cleavage. These experiments will help understand the role of YAP and Hippo pathway in controlling cell number during sea urchin development
Additional file 1 of Alteration in branching morphogenesis via YAP/TAZ in fibroblasts of fetal lungs in an LPS-induced inflammation model
No full textAdditional file 1: Figure S1. Representative immunocytochemistry staining of YAP, phosphorylated (p)-YAP, TAZ, and p-TAZ expressions in IMR-90 cells by lipopolysaccharide (LPS) at 0, 10, 30 and 50 μg/mL for 24 h. YAP and TAZ were stained in red, p-YAP and p-TAZ were stained in green, and nuclear staining were marked by DAPI in blue
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