A review of recent work on the discrete particle method at the University of Twente: an introduction to the open-source package MercuryDPM

In this paper we review some recent advances in DEM (DPM) modelling undertaken at the University of Twente. We introduce the new open-source package MercuryDPM that we have been developing over the last few years.\ud MercuryDPM is an object-oriented program with a simple C++ implementation and includes: support for moving and complex walls, such as polyhedra or screw-threads; state-of-the-art granular contact models; multi-species support; specialised classes, allowing the easy implementation of common geometries like chutes, hoppers, etc.; common handler interfaces for particles, walls and boundaries (so all type of objects are changed using the same interfaces); restarting; large self-test suite and numerous simple demos; and, visualisation support, both internal and using Visual Molecular Dynamics.\ud Additionally to these features, MercuryDPM has two major components that, to the best of our knowledge, cannot be found in other DPM packages. Firstly, it uses a novel advanced contact detection method that is able of dealing with multiple distinct granular components with sizes ranging over many orders of magnitude: the hierarchical grid. We explain how this algorithm works and demonstrate the speedup gained over the traditional linked cell approach. This algorithm has lower complexity for poly-dispersed ows which means for the first time large simulations with extremely wide size distributions are feasible.\ud Secondly, we present a novel way to extract continuum fields from discrete particle systems that is applicable to mixtures as well as boundaries and interfaces. The particle data is coarse grained in a way that is by construction compatible with the continuum equations of mass-, momentum-, and energy balance. Boundary interaction forces are taken into account in a self-consistent way and thus allow the construction of a continuous stress field even within one particle radius of the boundaries. The method does not require temporal averaging and thus can be used to investigate time-dependent flows as well as static and steady situations. This coarse-graining method is available from MercuryDPM either as a post-processing tool or it can be run in real time. In real-time mode, it not only reduces the data which has to be stored but also allows boundary conditions etc. to be updated depending on the current macroscopic state of the system, e.g. allowing the creation of a pressure-release wall.\ud Finally, we illustrate these tools and a selection of other features of MercuryDPM via various problems including size-driven segregation in chute flow, rotating drums, and screw-conveyer

Synthesis and evaluation in rats of homologous series of [F-18]-labeled dopamine D-2/3 receptor agonists based on the 2-aminomethylchroman scaffold as potential PET tracers

Background: Agonist positron emission tomography (PET) tracers for dopamine D-2/3 receptors (D(2/3)Rs) offer greater sensitivity to changes in endogenous dopamine levels than D2/3R antagonist tracers. D2/3R agonist tracers currently available for clinical research are labeled with the short-lived isotope carbon-11, which limits their use. We aimed to develop high-affinity D2R agonists amenable for labeling with the longer-living fluorine-18. Here, we report the evaluation as potential PET tracers of two homologous series of [F-18]fluorinated tracers based on the 2-aminomethylchroman-7-ol (AMC) scaffold: (R)-2-((4-(2-fluoroalkoxy)benzylamino)methyl)chroman-7-ols (AMC13 homologues) and (R)-2-((2-(4-(4-(fluoroalkoxy)phenyl)piperazin-1-yl)ethylamino)methyl)chroman-7-ols (AMC15 homologues). We varied the length of the F-18-fluoroalkyl chain in these structures to balance brain penetration and non-specific binding of the radioligands by adjusting their lipophilicity. Methods: The tracers were evaluated in brain slices of Sprague-Dawley rats by in vitro autoradiography and in living rats by microPET imaging and ex vivo autoradiography. PET data were analyzed with one- and two-tissue compartmental models (1TCM/2TCM), simplified reference tissue model (SRTM), and Logan graphical analysis. Specificity of binding was tested by blocking D2/3R with raclopride. Results: Homologues with a shorter fluoroalkyl chain consistently showed greater D2/3R-specific-to-total binding ratios in the striatum than those with longer chains. The fluoroethoxy homologue of AMC13 ([F-18]FEt-AMC13) demonstrated the highest degree of D2/3R-specific binding among the evaluated tracers: mean striatum-to-cerebellum uptake ratio reached 4.4 in vitro and 2.1/2.8 in vivo/ex vivo (PET/autoradiography). Striatal binding potential (BPND) relative to cerebellum was 0.51-0.63 depending on the estimation method. Radiometabolites of [F-18]FEt-AMC13 did not enter the brain. In vitro, application of 10 mu mol/L raclopride reduced D2/3R-specific binding of [F-18]FEt-AMC13 in the striatum by 81 %. In vivo, pre-treatment with 1 mg/kg (2.9 mu mol/kg) raclopride led to 17-39 % decrease in D2/3R-specific binding in the striatum. Conclusions: Varying the length of the [F-18]fluoroalkyl chain helped improve the characteristics of the original candidate tracers. Further modifications of the current lead [F-18]FEt-AMC13 can provide an agonist radiopharmaceutical suitable for D2/3R imaging by PET

Resistance to tumor necrosis factor (TNF) cytotoxicity by autocrine TNF production is independent of intracellular signaling pathways.

AbstractWe previously showed that autocrine tumor necrosis factor (TNF) production in the TNF-sensitive L929sA fibrosarcoma cell line induced TNF resistance, which is correlated with downmodulation of both TNF receptors on the cell surface. We now analyzed whether autocrine TNF production also interfered with intracellular TNF signaling pathways. The L929sA-CAT-R55i cell line, in which cell death can be induced by controlled cytoplasmic expression of a trimeric fusion protein between chloramphenicol acetyltransferase and the intracellular domain of TNF-R55 (CAT-R55i), was supertransfected with the murine TNF gene. Expression of the latter conferred resistance to cell death induced by exogenous TNF, while cytotoxicity induced by CAT-R55i was not impaired. This demonstrates that autocrine TNF did not induce intracellular mechanisms that block TNF signaling leading to cell death. Thus the induction of TNF resistance via autocrine TNF production in L929sA cells is solely due to downmodulation of TNF receptors on the cell surface

TMC125 Displays a High Genetic Barrier to the Development of Resistance: Evidence from In Vitro Selection Experiments

TMC125 is a potent new investigational nonnucleoside reverse transcriptase inhibitor (NNRTI) that is active against human immunodeficiency virus type 1 (HIV-1) with resistance to currently licensed NNRTIs. Sequential passage experiments with both wild-type virus and NNRTI-resistant virus were performed to identify mutations selected by TMC125 in vitro. In addition to “classic” selection experiments at a low multiplicity of infection (MOI) with increasing concentrations of inhibitors, experiments at a high MOI with fixed concentrations of inhibitors were performed to ensure a standardized comparison between TMC125 and current NNRTIs. Both low- and high-MOI experiments demonstrated that the development of resistance to TMC125 required multiple mutations which frequently conferred cross-resistance to efavirenz and nevirapine. In high-MOI experiments, 1 μM TMC125 completely inhibited the breakthrough of resistant virus from wild-type and NNRTI-resistant HIV-1, in contrast to efavirenz and nevirapine. Furthermore, breakthrough of virus from site-directed mutant (SDM) SDM-K103N/Y181C occurred at the same time or later with TMC125 as breakthrough from wild-type HIV-1 with efavirenz or nevirapine. The selection experiments identified mutations selected by TMC125 that included known NNRTI-associated mutations L100I, Y181C, G190E, M230L, and Y318F and the novel mutations V179I and V179F. Testing the antiviral activity of TMC125 against a panel of SDMs indicated that the impact of these individual mutations on resistance was highly dependent upon the presence and identity of coexisting mutations. These results demonstrate that TMC125 has a unique profile of activity against NNRTI-resistant virus and possesses a high genetic barrier to the development of resistance in vitro

Synthesis and evaluation in rats of the dopamine D2/3 receptor agonist 18F-AMC20 as a potential radioligand for PET

Dopamine D(2/3) receptor (D(2/3)R) agonist PET tracers are better suited for the imaging of synaptic dopaminergic neurotransmission than D(2/3)R antagonists and may also offer the opportunity to study in vivo the high-affinity state of D(2/3)R (D(2/3)RHigh). With the aim to develop (18)F-labeled D2/3R agonists suitable for widespread clinical application, we report here on the synthesis and in vitro and in vivo evaluation of a D(2/3)R agonist ligand from the aminomethyl chromane (AMC) class-(R)-2-[(4-(18)F-fluorobenzylamino)methyl]chroman-7-ol ((18)F- AMC20: ). In vitro affinities of AMC20: toward dopaminergic receptor subtypes were measured in membrane homogenates prepared from HEK293 cells expressing human dopamine receptors. Agonism of AMC20: was assessed in the arrestin recruitment assay in Chinese hamster ovary-K(1) cells expressing the long isoform of D(2)R (D(2)RLong). D(2/3)R-specific binding of (18)F- AMC20: was evaluated in brain slices of Sprague-Dawley rats by in vitro autoradiography and in living rats by in vivo small-animal PET imaging and ex vivo autoradiography. PET data were analyzed with 1- and 2-tissue compartmental models, the simplified reference tissue model, and Logan graphical analysis. Specificity of binding was tested by blocking D(2/3)R with raclopride (coincubation with 10 μM in vitro, administration of 1.0 mg/kg in vivo). In membrane homogenates, AMC20: demonstrated picomolar affinity at D(2)RHigh (mean inhibition constant [K(i)] = 85 pM) and excellent selectivity against the low-affinity state of D(2)R (D(2)RLow) (mean K(i) = 84 nM, 988-fold selectivity) and D(1)-like receptors (mean K(i) = 5,062 nM at D1R). The efficacy of AMC20: was 90% of that of dopamine in the arrestin recruitment assay. Up to 70% of total binding of (18)F- AMC20: in the D2/3R-rich striatum in rat brain slices was D(2/3)R-specific; in living rats, the uptake ratio between the striatum and the D(2/3)R-poor cerebellum reached 2.0-2.5, depending on the measurement method. Radiometabolites of (18)F- AMC20: did not enter the brain. Striatal binding potential of (18)F- AMC20: varied between 0.49 and 0.59 depending on the estimation method. Pretreatment with 1 mg of raclopride per kilogram reduced the apparent specific binding of (18)F- AMC20: in the striatum. (18)F- AMC20: shows specific binding to D(2/3)R in the striatum of living rats. Further optimization of the chemical structure of (18)F- AMC20: can lead to (18)F-labeled D(2/3) agonist PET tracers more suitable for in vivo clinical applicatio

L1 knockout mice show dilated ventricles, vermis hypoplasia and impaired exploration patterns

L1 is a neural cell adhesion molecule mainly involved in axon guidance and neuronal migration during brain development. Mutations in the human L1 gene give rise to a complex clinical picture, with mental retardation, neurologic abnormalities and a variable degree of hydrocephalus. Recently, a transgenic mouse model with a targeted null mutation in the L1 gene was generated. These knockout (KO) mice show hypoplasia of the corticospinal tract. Here we have performed further studies of these KO mice including magnetic resonance imaging of the brain, neuropathological analysis and behavioral testing. The ventricular system was shown to be abnormal with dilatation of the lateral ventricles and the 4th ventricle, and an altered shape of the Sylvius aqueduct. Additionally, the cerebellar vermis of the KO mice is hypoplastic. Their exploratory behavior is characterized by stereotype peripheral circling reminiscent of that of rodents with induced cerebellar lesions