Assessing the precision of model predictions and other functions of model parameters

Models fitted to data are used extensively in chemical engineering for a variety of purposes, including simulation, design and control. In any of these contexts it is important to assess the uncertainties in the estimated parameters and in any functions of these parameters, including predictions from the fitted model. Profiling is a likelihood ratio approach to estimating uncertainties in parameters and functions of parameters. A comparison is made between the optimization and reparameterization approaches to determining likelihood intervals for functions of parameters. The merits and limitations of generalized profiling are discussed in relation to the linearization approach commonly used in engineering. The benefits of generalized profiling are illustrated with two examples. A geometric interpretation of profiling is used to elucidate its value, and cases are identified for which the numerical algorithm fails. An alternative approach is suggested for these cases.     

Modeling of gas diffusion layers with curved fibers using a genetic algorithm

This paper presents a methodology for modeling microstructures of fibrous porous media with curved fibers. The developed methodology utilizes implicit periodic surface model coupled with the genetic algorithm (GA) optimization to construct the porous microstructures. The fibers profile is represented by the periodic implicit surfaces and their orientation and curvature are determined by GA optimization. To reconstruct the microstructures with higher resemblance to the actual porous media GA is utilized to minimize the fibers stored strain energy and their intersection volumes. Coupling the image processing techniques to the geometry construction procedure the morphological and transport properties of the constructed microstructures are also determined. To verify the feasibility and the accuracy of the proposed methodology the microstructure of Freudenberg H2315 GDL is constructed and characterized. The presented methodology enables a parametric design approach. Thus, the effects of the microstructure's properties e.g., fibers diameter, fibers orientation and porosity of the porous structure on the transport properties of the fibrous media are investigated.     

ELTD1 Activation Induces an Endothelial-EMT Transition to a Myofibroblast Phenotype

ELTD1 is expressed in endothelial and vascular smooth muscle cells and has a role in angiogenesis. It has been classified as an adhesion GPCR, but as yet, no ligand has been identified and its function remains unknown. To establish its role, ELTD1 was overexpressed in endothelial cells. Expression and consequently ligand independent activation of ELTD1 results in endothelial-mesenchymal transistion (EndMT) with a loss of cell-cell contact, formation of stress fibres and mature focal adhesions and an increased expression of smooth muscle actin. The effect was pro-angiogenic, increasing Matrigel network formation and endothelial sprouting. RNA-Seq analysis after the cells had undergone EndMT revealed large increases in chemokines and cytokines involved in regulating immune response. Gene set enrichment analysis of the data identified a number of pathways involved in myofibroblast biology suggesting that the endothelial cells had undergone a type II EMT. This type of EMT is involved in wound repair and is closely associated with inflammation implicating ELTD1 in these processes.     

Quality assurance of PASADENA hyperpolarization for 13C biomolecules

Object  Define MR quality assurance procedures for maximal PASADENA hyperpolarization of a biological ¹³C molecular imaging reagent. Materials and methods  An automated PASADENA polarizer and a parahydrogen generator were installed. ¹³C enriched hydroxyethyl acrylate, 1-¹³C, 2,3,3-d₃ (HEA), was converted to hyperpolarized hydroxyethyl propionate, 1-¹³C, 2,3,3-d₃ (HEP) and fumaric acid, 1-¹³C, 2,3-d₂ (FUM) to hyperpolarized succinic acid, 1-¹³C, 2,3-d₂ (SUC), by reaction with parahydrogen and norbornadiene rhodium catalyst. Incremental optimization of successive steps in PASADENA was implemented. MR spectra and in vivo images of hyperpolarized ¹³C imaging agents were acquired at 1.5 and 4.7 T. Results  Application of quality assurance (QA) criteria resulted in incremental optimization of the individual steps in PASADENA implementation. Optimal hyperpolarization of HEP of P = 20% was achieved by calibration of the NMR unit of the polarizer (B ₀ field strength ± 0.002 mT). Mean hyperpolarization of SUC, P = [15.3 ± 1.9]% (N = 16) in D ₂O, and P = [12.8 ± 3.1]% (N = 12) in H ₂O, was achieved every 5–8 min (range 13–20%). An in vivo ¹³C succinate image of a rat was produced. Conclusion  PASADENA spin hyperpolarization of SUC to 15.3% in average was demonstrated (37,400 fold signal enhancement at 4.7 T). The biological fate of ¹³C succinate, a normally occurring cellular intermediate, might be monitored with enhanced sensitivity.     

Time‐mode circuits for analog computation

We introduce time‐mode circuits, a set of basic circuit building blocks for analog computation using a temporal step function representation for the inputs and outputs. These novel time‐mode circuits are low power, provide good noise performance and offer improved dynamic range. The design, IC implementation and detailed theoretical signal‐to‐noise ratio (SNR) analysis of a prototype time‐mode circuit—a weighted average computation circuit—are discussed. This new way of computation is studied with respect to existing conventional voltage‐mode and current‐mode circuits. Two possible applications of these time‐mode circuits are presented: an edge detection circuit for 16 pixels and a 3‐tap FIR filter that provides an SNR of 64 dB. Copyright © 2008 John Wiley & Sons, Ltd.     

Optically trapping confocal Raman microscopy of individual lipid vesicles: kinetics of phospholipase A(2)-catalyzed hydrolysis of phospholipids in the membrane bilayer

Phospholipase A2 (PLA2)-catalyzed hydrolysis at the sn-2 position of 1,2-dimyristoyl-sn-glycero-3-phosphocholine in optically trapped liposomes is monitored in situ using confocal Raman microscopy. Individual optically trapped liposomes (0.6 microm in diameter) are exposed to PLA2 isolated from cobra (Naja naja naja) venom at varying enzyme concentrations. The relative Raman scattering intensities of C-C stretching vibrations from the trans and gauche conformers of the acyl chains are correlated directly with the extent of hydrolysis, allowing the progress of the reaction to be monitored in situ on a single vesicle. In dilute vesicle dispersions, the technique allows the much higher local concentration of lipid molecules in a single vesicle to be detected free of interferences from the surrounding solution. Observing the local composition of an optically trapped vesicle also allows one to determine whether the products of enzyme-catalyzed hydrolysis remain associated with the vesicle or dissolve into solution. The observed reaction kinetics exhibited a time lag prior to the rapid hydrolysis. The lag time varied inversely with the enzyme concentration, which is consistent with the products of enzyme-catalyzed lipid hydrolysis reaching a critical concentration that allows the enzyme to react at a much faster rate. The turnover rate of membrane-bound enzyme determined by Raman microscopy during the rapid, burst-phase kinetics was 1200 s(-1). Based on previous measurements of the equilibrium for PLA2 binding to lipid membranes, the average number of enzyme molecules responsible for catalyzing the hydrolysis of lipid on a single optically trapped vesicle is quite small, only two PLA2 molecules at the lowest enzyme concentration studied.     

Rapid assessment of the physiological status of Streptococcus macedonicus by flow cytometry and fluorescence probes

Flow cytometry in combination with fluorescence probes was applied to rapidly assess the physiological status of Streptococcus macedonicus ACA-DC 198, a newly described member of the lactic acid bacteria group with technologically important features (e.g. lantibiotic production). A sonication procedure was developed for disaggregating typical streptococci chains in order to optimize cell preparations for single cell analysis. Single stained live and dead populations of S. macedonicus cells were clearly resolved based on membrane potential by bis-oxonol [DiBAC(4)(3)], membrane integrity by Propidium Iodide (PI) and enzymatic activity as well as membrane integrity by Carboxyfluorescein Diacetate (cFDA). Further, estimation of both live and dead cells by a cFDA/PI two-colour flow cytometric assay showed excellent correlation with the dead cells in the samples (dead(FCM)=0.9945 dead(S)-0.806, R(2)=0.9986 and live(FCM)=-0.978 dead(S)+98.895, R(2)=0.9992). Finally, the assay was applied to study the physiology of S. macedonicus after acid stress. Interestingly, in situ assessment of the physiological status of stressed S. macedonicus cells by flow cytometry and single cell sorting revealed the coexistence of three distinct subpopulations according to their fluorescence labelling behaviour and culturability, representing intact/culturable, permeabilized/dead and potentially injured cells with the latter exhibiting both metabolic activity and membrane permeabilization as well as decreased culturability.     

Modelling the biomechanical properties of DNA using computer simulation

Duplex DNA must remain stable when not in use to protect the genetic material. However, the two strands must be separated whenever genes are copied or expressed to expose the coding strand for synthesis of complementary RNA or DNA bases. Therefore, the double stranded structure must be relatively easy to take apart when required. These conflicting biological requirements have important implications for the mechanical properties of duplex DNA. Considerable insight into the forces required to denature DNA has been provided by nanomanipulation experiments, which measure the mechanical properties of single molecules in the laboratory. This paper describes recent computer simulation methods that have been developed to mimic nanomanipulation experiments and which, quite literally, 'destruction test' duplex DNA in silico. The method is verified by comparison with single molecule stretching experiments that measure the force required to unbind the two DNA strands. The model is then extended to investigate the thermodynamics of DNA bending and twisting. This is of biological importance as the DNA must be very tightly packaged to fit within the nucleus, and is therefore usually found in a highly twisted or supercoiled state (in bacteria) or wrapped tightly around histone proteins into a densely compacted structure (in animals). In particular, these simulations highlight the importance of thermal fluctuations and entropy in determining the biomechanical properties of DNA. This has implications for the action of DNA processing molecular motors, and also for nanotechnology. Biological machines are able to manipulate single molecules reliably on an energy scale comparable to that of thermal noise. The hope is that understanding the statistical mechanisms that a cell uses to achieve this will be invaluable for the future design of 'nanoengines' engineered to perform new technological functions at the nanoscale.