FLAMINGO: calibrating large cosmological hydrodynamical simulations with machine learning

To fully take advantage of the data provided by large-scale structure surveys, we need to quantify the potential impact of baryonic effects, such as feedback from active galactic nuclei (AGN) and star formation, on cosmological observables. In simulations, feedback processes originate on scales that remain unresolved. Therefore, they need to be sourced via subgrid models that contain free parameters. We use machine learning to calibrate the AGN and stellar feedback models for the FLAMINGO (Fullhydro Large-scale structure simulations with All-sky Mapping for the Interpretation of Next Generation Observations) cosmological hydrodynamical simulations. Using Gaussian process emulators trained on Latin hypercubes of 32 smaller volume simulations, we model how the galaxy stellar mass function (SMF) and cluster gas fractions change as a function of the subgrid parameters. The emulators are then fit to observational data, allowing for the inclusion of potential observational biases. We apply our method to the three different FLAMINGO resolutions, spanning a factor of 64 in particle mass, recovering the observed relations within the respective resolved mass ranges. We also use the emulators, which link changes in subgrid parameters to changes in observables, to find models that skirt or exceed the observationally allowed range for cluster gas fractions and the SMF. Our method enables us to define model variations in terms of the data that they are calibrated to rather than the values of specific subgrid parameters. This approach is useful, because subgrid parameters are typically not directly linked to particular observables, and predictions for a specific observable are influenced by multiple subgrid parameters.

Human osteogenesis involves differentiation-dependent increases in the morphogenically active 3' alternative splicing variant of acetylcholinesterase

The extended human acetylcholinesterase (AChE) promoter contains many binding sites for osteogenic factors, including 1,25-(OH)2 vitamin D3 and 17beta-estradiol. In differentiating osteosarcoma Saos-2 cells, both of these factors enhanced transcription of the AChE mRNA variant 3' terminated with exon 6 (E6-AChE mRNA), which encodes the catalytically and morphogenically active E6-AChE isoform. In contrast, antisense oligodeoxynucleotide suppression of E6-AChE mRNA expression increased Saos-2 proliferation in a dose- and sequence-dependent manner. The antisense mechanism of action was most likely mediated by mRNA destruction or translational arrest, as cytochemical staining revealed reduction in AChE gene expression. In vivo, we found that E6-AChE mRNA levels rose following midgestation in normally differentiating, postproliferative fetal chondrocytes but not in the osteogenically impaired chondrocytes of dwarf fetuses with thanatophoric dysplasia. Taken together, these findings suggest morphogenic involvement of E6-AChE in the proliferation-differentiation balance characteristic of human osteogenesis.

The incapability of interleukin-4 to induce AP-1 activity in murine mast cells

The results presented in this study shed new light on the molecular mechanism responsible for the control of interleukin (IL)-3- and IL-4 mediated mast cell proliferation. By measurements of AP-1 DNA-binding activity, it was found that IL-3 induced such activity while IL-4 did not. This difference in the pattern of AP-1 DNA-binding activity induced by each lymphokine indicates the differential involvement of AP-1 in the different proliferative responses of mast cells to IL-3 and IL-4.

Enhancement of interleukin-3-dependent mast cell proliferation by suppression of c-jun expression

We have previously shown that protein kinase C (PKC) depletion is associated with an increase in the proliferation of interleukin 3 (IL-3)-induced mast cells. Here we show that the AP-1 components c-Jun and c-Fos are induced by IL-3. While c-Jun's induction by IL-3 is totally dependent on PKC, c-Fos induction by IL-3 is only attenuated by PKC depletion. AP-1 binding activity was also induced by IL-3 but this induction was PKC independent. These results indicated a possible involvement of c-Jun in the inhibition of IL-3-induced growth regulation. A support for this assumption came from experiments in which an increase in thymidine incorporation into mast cells was noted when c-jun antisense oligomers were administered to IL-3-treated cells. Since the only known effect of direct inhibition of c-Jun on proliferation rates in several cellular systems was a reduction of proliferation, we verified that our c-jun antisense oligomer could also inhibit proliferation rates in fibroblasts where such a repression was previously reported. Thus c-Jun has an inhibitory effect on IL-3 induction of mast cells proliferation that is distinct from its role in several other cellular environments. These observations reveal the involvement of AP-1 and its components in IL-3-induced signal transduction and the importance of the mast cell environment in determining their specific cellular function.

Protein kinase C plays an inhibitory role in interleukin 3- and interleukin 4-mediated mast cell proliferation

Interleukin 3 (IL-3) is required for the survival and proliferation of mouse bone marrow derived mast cells (BMMC). Although interleukin 4 (IL-4) has no direct effect on growth activity, it synergizes with IL-3 in promoting the growth of these cells. The intracellular mechanism by which these ligand-receptor interactions promote mast cell growth are not well documented in the literature. Here we present evidence that both IL-3 and IL-4 have been found to activate protein kinase C (PKC) and phosphatidylinositol turnover in BMMC, in a similar time- and dose-dependent manner, indicating that activation of PKC is not sufficient to induce proliferation in these cells. In this work we addressed the question as to whether the activation of PKC is necessary for mast cell proliferation. Activation of PKC by phorbol myristate acetate causes inhibition of IL-3-mediated growth for the first 72 h of incubation. The inhibition in IL-3-mediated proliferation gradually lessens with the stages of PKC depletion, which is complete after 72 h. The enhancement in phorbol myristate acetate-treated cells grows as PKC is depleted. The inactive phorbol ester, 4-alpha-phorbol, had no effect on proliferation of BMMC. Cells, PKC-depleted by chronical phorbol ester treatment, responded to IL-3 or IL-4 with a significant increase in [3H] thymidine uptake over PKC containing cells stimulated with the same lymphokine. Use of antibodies to these lymphokines showed that the enhanced response of the PKC-depleted BMMC was not due to the additional autocrine production of IL-3 or IL-4 by these cells. The PKC-depleted cells retain the capacity to return to almost normal levels of PKC activity and sensitivity to IL-3 and IL-4, after 72 and 120 h, respectively. These results indicate that PKC plays an important inhibitory role in IL-3- and IL-4-mediated proliferation of BMMC.