Stereoscopic cell visualization: from mesoscopic to molecular scale

Sommer B, Bender C, Hoppe T, Gamroth C, Jelonek L. Stereoscopic cell visualization: from mesoscopic to molecular scale. Journal of Electronic Imaging. 2014;23(1): 11007

Grid Workflow Approach using the CELLmicrocosmos 2.2 MembraneEditor and UNICORE to commit and monitor GROMACS Jobs

Rubert S, Gamroth C, Krüger J, Sommer B. Grid Workflow Approach using the CELLmicrocosmos 2.2 MembraneEditor and UNICORE to commit and monitor GROMACS Jobs. In: Warzecha K-D, Packschies L, eds. CEUR Workshop Proceedings. Vol 826. CEUR-WS; 2012.Molecular dynamic simulations of membrane systems are an important method for the prediction and analysis of physicochemical properties. The CELLmicrocosmos 2.2 MembraneEditor (CmME) provides a comfortable workflow to generate lipid membranes with different conformations. While CmME is intended to generate molecular structures on desktop and mobile computers in a very short time, the atomic simulation of exported membranes needs external high performance computer resources. In this work, a first approach of a direct connection between CmME and a cluster running GROMACS using the Gridmiddleware UNICORE-6 is discussed

CELLmicrocosmos 2.2 Membrane Editor: A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems

Sommer B, Dingersen T, Gamroth C, et al. CELLmicrocosmos 2.2 Membrane Editor: A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems. Journal of Chemical Information and Modeling. 2011;51(5):1165-1182.New perspectives have been developed to understand the processes of modeling heterogeneous membranes. These are crucial steps prior to applying advanced techniques like molecular dynamic simulations of whole membrane systems. Lipid, protein, and membrane packing problems are addressed based on biochemical properties in combination with computational optimization techniques. The CELLmicrocosmos 2.2 MembraneEditor (CmME) is introduced as an appropriate framework to handle such problems by offering diverse algorithmic approaches. Its algorithm plug-in-interface enables modelers to generate problem-specific algorithms. Good solutions concerning runtime and lipid density are realized by focusing on the outer shapes of the PDB-based molecules. Application cases are presented like the publication-based modeling of inner and outer mitochondrial membrane-fragments, semiautomatic incorporation of proteins, and the assembly of rafts. Concerning geometrical aspects of the lipids, the achieved results are consistent with experimental observations related to lipid densities and distributions. Finally, two membranes simulated with GROMACS are analyzed and compared: the first is generated with conventional scripting techniques, the second with the CmME Distributor algorithm. The examples prove that CmME is a valuable and versatile tool for a broad set of applications in analysis and visualization of biomembranes

Regulating Innovation, Trade and Uncertain Risks - Full copy

MaRBLe Research Papers Maastricht Research-Based Learning Project (MaRBLe) Faculty of Law and Faculty of Arts and Social Sciences Maastricht University, 201

Ventilatory settings in the initial 72 h and their association with outcome in out-of-hospital cardiac arrest patients: a preplanned secondary analysis of the targeted hypothermia versus targeted normothermia after out-of-hospital cardiac arrest (TTM2) trial

International audienc

Oxygen targets and 6-month outcome after out of hospital cardiac arrest: a pre-planned sub-analysis of the targeted hypothermia versus targeted normothermia after Out-of-Hospital Cardiac Arrest (TTM2) trial

International audienceAbstract Background Optimal oxygen targets in patients resuscitated after cardiac arrest are uncertain. The primary aim of this study was to describe the values of partial pressure of oxygen values (PaO 2 ) and the episodes of hypoxemia and hyperoxemia occurring within the first 72 h of mechanical ventilation in out of hospital cardiac arrest (OHCA) patients. The secondary aim was to evaluate the association of PaO 2 with patients’ outcome. Methods Preplanned secondary analysis of the targeted hypothermia versus targeted normothermia after OHCA (TTM2) trial. Arterial blood gases values were collected from randomization every 4 h for the first 32 h, and then, every 8 h until day 3. Hypoxemia was defined as PaO 2  300 mmHg. Mortality and poor neurological outcome (defined according to modified Rankin scale) were collected at 6 months. Results 1418 patients were included in the analysis. The mean age was 64 ± 14 years, and 292 patients (20.6%) were female. 24.9% of patients had at least one episode of hypoxemia, and 7.6% of patients had at least one episode of severe hyperoxemia. Both hypoxemia and hyperoxemia were independently associated with 6-month mortality, but not with poor neurological outcome. The best cutoff point associated with 6-month mortality for hypoxemia was 69 mmHg (Risk Ratio, RR = 1.009, 95% CI 0.93–1.09), and for hyperoxemia was 195 mmHg (RR = 1.006, 95% CI 0.95–1.06). The time exposure, i.e., the area under the curve (PaO 2 -AUC), for hyperoxemia was significantly associated with mortality ( p = 0.003). Conclusions In OHCA patients, both hypoxemia and hyperoxemia are associated with 6-months mortality, with an effect mediated by the timing exposure to high values of oxygen. Precise titration of oxygen levels should be considered in this group of patients. Trial registration : clinicaltrials.gov NCT02908308 , Registered September 20, 2016