Abstract. In this paper we present the current version of the Parallelized Large-Eddy Simulation Model (PALM) whose core has been developed at the Institute of Meteorology and Climatology at Leibniz Universität Hannover (Germany). PALM is a Fortran 95-based code with some Fortran 2003 extensions and has been applied for the simulation of a variety of atmospheric and oceanic boundary layers for more than 15 years. PALM is optimized for use on massively parallel computer architectures and was recently ported to general-purpose graphics processing units. In the present paper we give a detailed description of the current version of the model and its features, such as an embedded Lagrangian cloud model and the possibility to use Cartesian topography. Moreover, we discuss recent model developments and future perspectives for LES applications.

The ATPase retinoid acid-inducible gene (RIG)-I senses viral RNA in the cytoplasm of infected cells and subsequently activates cellular antiviral defense mechanisms. RIG-I recognizes molecular structures that discriminate viral from host RNA. Here, we show that RIG-I ligands require base-paired structures in conjunction with a free 5-triphosphate to trigger antiviral signaling. Hitherto unavailable chemically synthesized 5-triphosphate RNA ligands do not trigger RIG-I-dependent IFN production in cells, and they are unable to trigger the ATPase activity of RIG-I without a base-paired stretch. Consistently, immunostimulatory RNA from cells infected with a virus recognized by RIG-I is sensitive to double-strand, but not single-strand, specific RNases. In vitro, base-paired stretches and the 5-triphosphate bind to distinct sites of RIG-I and synergize to trigger the induction of signaling competent RIG-I multimers. Strengthening our model of a bipartite molecular pattern for RIG-I activation, we show that the activity of supposedly ''single-stranded'' 5-triphosphate RNAs generated by in vitro transcription depends on extended and base-paired by-products inadvertently, but commonly, produced by this method. Together, our findings accurately define a minimal molecular pattern sufficient to activate RIG-I that can be found in viral genomes or transcripts.immunostimulatory RNA ͉ melanoma differentiation-associated protein 5 ͉ retinoid acid-inducible gene-I-like helicases ͉ virus infection ͉ interferon production

Survival of plasma cells is regulated by B-cell maturation antigen (BCMA), a membrane-bound receptor activated by its agonist ligands BAFF and APRIL. Here we report that γ-secretase directly cleaves BCMA, without prior truncation by another protease. This direct shedding is facilitated by the short length of BCMA's extracellular domain. In vitro, γ-secretase reduces BCMA-mediated NF-κB activation. In addition, γ-secretase releases soluble BCMA (sBCMA) that acts as a decoy neutralizing APRIL. In vivo, inhibition of γ-secretase enhances BCMA surface expression in plasma cells and increases their number in the bone marrow. Furthermore, in multiple sclerosis, sBCMA levels in spinal fluid are elevated and associated with intracerebral IgG production; in systemic lupus erythematosus, sBCMA levels in serum are elevated and correlate with disease activity. Together, shedding of BCMA by γ-secretase controls plasma cells in the bone marrow and yields a potential biomarker for B-cell involvement in human autoimmune diseases.

Abstract. In this paper, we describe the PALM model system 6.0. PALM (formerly an abbreviation for Parallelized Large-eddy Simulation Model and now an independent name) is a Fortran-based code and has been applied for studying a variety of atmospheric and oceanic boundary layers for about 20 years. The model is optimized for use on massively parallel computer architectures. This is a follow-up paper to the PALM 4.0 model description in Maronga et al. (2015). During the last years, PALM has been significantly improved and now offers a variety of new components. In particular, much effort was made to enhance the model with components needed for applications in urban environments, like fully interactive land surface and radiation schemes, chemistry, and an indoor model. This paper serves as an overview paper of the PALM 6.0 model system and we describe its current model core. The individual components for urban applications, case studies, validation runs, and issues with suitable input data are presented and discussed in a series of companion papers in this special issue.

The effect of anthropogenic aerosol on the reflectivity of stratocumulus cloud decks through changes in cloud amount is a major uncertainty in climate projections. In frequently occurring nonprecipitating stratocumulus, cloud amount can decrease through aerosol-enhanced cloud-top mixing. The climatological relevance of this effect is debated because ship exhaust only marginally reduces stratocumulus amount. By comparing detailed numerical simulations with satellite analyses, we show that ship-track studies cannot be generalized to estimate the climatological forcing of anthropogenic aerosol. The ship track–derived sensitivity of the radiative effect of nonprecipitating stratocumulus to aerosol overestimates their cooling effect by up to 200%. The offsetting warming effect of decreasing stratocumulus amount needs to be taken into account if we are to constrain the cloud-mediated radiative forcing of anthropogenic aerosol.

Acute and chronic neurodegeneration, for example, following brain injury or Alzheimer's disease, is characterized by programmed death of neuronal cells. The present study addresses the role and interaction of p53-and NF-jB-dependent mechanisms in delayed neurodegeneration following traumatic brain injury (TBI). After experimental TBI in mice p53 rapidly accumulated in the injured brain tissue and translocated to the nucleus of damaged neurons, whereas NF-jB transcriptional activity simultaneously declined. Post-traumatic neurodegeneration correlated with the increase in p53 levels and was significantly reduced by the selective p53 inhibitor pifithrin-a (PFT). Strikingly, this protective effect was observed even when PFT treatment was delayed up to 6 h after trauma. Inhibition of p53 activity resulted in the concomitant increase in NF-jB transcriptional activity and upregulation of NF-jB-target proteins, for example X-chromosomal-linked inhibitor of apoptosis (XIAP). It is interesting to note that inhibition of XIAP abolished the neuroprotective effects of PFT in cultured neurons exposed to camptothecin, glutamate, or oxygen glucose deprivation. In conclusion, delayed neuronal cell death after brain trauma is mediated by p53-dependent mechanisms that involve inhibition of NF-jB transcriptional activity. Hence, p53 inhibition provides a promising approach for the treatment of acute brain injury, since it blocks apoptotic pathways and concomitantly triggers survival signaling with a therapeutic window relevant for clinical applications.

BAFF and APRIL, which control B-cell homeostasis, are therapeutic targets in autoimmune diseases. TACI-Fc (atacicept), a soluble fusion protein containing the extracellular domain of the BAFF-APRIL-receptor TACI, was applied in clinical trials. However disease activity in multiple sclerosis (MS) unexpectedly increased, whereas in systemic lupus erythematosus (SLE) atacicept was beneficial. Here, we show that an endogenous soluble form of TACI exists in vivo. TACI proteolysis involved shedding by ADAM10 releasing sTACI from activated B cells. The membrane-bound stub was subsequently cleaved by γ-secretase reducing ligand-independent signaling of the remaining C-terminal fragment. The shed ectodomain assembled ligand-independently in a homotypic way. It functioned as a decoy receptor inhibiting BAFF- and APRIL-mediated B-cell survival and NFκB-activation. We determined sTACI levels in autoimmune diseases with established hyper-activation of the BAFF-APRIL system. sTACI levels were elevated both in the cerebrospinal fluid (CSF) of the brain-restricted autoimmune disease MS correlating with intrathecal IgG production, as well as in the serum of the systemic autoimmune disease SLE correlating with disease activity. Together, we show that TACI is sequentially processed by ADAM10 and γ-secretase. The released sTACI is an immunoregulator that shares decoy functions with atacicept. Itreflectssystemic and compartmentalized B-cell accumulation and activation.

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