A refined circular template matching method for classification of human cytomegalovirus capsids in TEM images

An automatic image analysis method for describing, segmenting, and classifying human cytomegalovirus capsids in transmission electron micrograph (TEM) images of host cell nuclei has been developed. Three stages of the capsid assembly process in the host cell nucleus have been investigated. Each class is described by a radial density profile, which is the average grey-level at each radial distance from the center. A template, constructed from the profile, is used to find possible capsid locations by correlation based matching. The matching results are further refined by size and distortion analysis of each possible capsid, resulting in a final segmentation and classification.     

Atmospheric transport of polybrominated diphenyl ethers and polychlorinated biphenyls to the Baltic Sea

The atmospheric transport of polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) was compared by measuring concentrations in air and deposition on an island located in the central basin of the Baltic Sea. Median sigmaPBDE and sigmaPCB concentrations (gaseous + particle) were 8.6 and 7.4 pg m(-3), respectively. Airborne PCBs were mainly found in the gaseous phase, while most of the PBDEs were detected on particles, which agrees with predicted particle/gas distributions. SigmaPBDE levels were dominated by the decabrominated BDE209 followed bythe tetrabrominated BDE47 and pentabrominated BDE99. BDE209 is a marker for the environmental distribution of the commercial deca-BDE formulation (>99.5% BDE209), whereas BDE47 and BDE99 are markers for the commercial penta-BDE mixture. General correlations between PBDEs and PCBs suggested similarities in sources and transport mechanism, while more detailed examination of the data identified notable behaviors and exceptions. Differences in regression slopes among tetra-, penta-, and decabrominated PBDEs may reflect different transport processes and the change in usage pattern. Tetra- and pentabrominated PBDEs may originate from secondary sources such as air surface exchange in a manner similar to that of the PCBs, while the deca-BDE209 formulation still has primary sources. The tribrominated BDE17 was also detected and is proposed to be a breakdown product due to atmospheric debromination processes. PBDEs had higher washout ratios than PCBs, explaining their higher concentrations compared to PCBs in precipitation (median of 6.0 and 0.5 ng L(-1) for sigmaBDE and sigmaPCB concentrations ("dissolved" + particle), respectively) than in air. The calculated yearly deposition of PBDEs and PCBs indicated that the atmospheric input of PBDEs to the Baltic Proper is currently exceeding that of the PCBs by a factor of 40, while that of the PCBs is decreasing.     

Visualization of a pharmaceutical unit operation: wet granulation

Recent developments in the field of process engineering and manufacturing sciences enable a new level of process understanding. However, extracting this understanding from increasing amounts of information is challenging. The aim of this study was to create a process vector from a model process describing all relevant information and, by that means, create a tool for combining and visualizing this information. Physical (impeller torque and temperature) and chemical (near-infrared spectroscopy) information from a small-scale high-shear granulation was used in the process vector. The vectors created were visualized by two different methods: principal component analysis (PCA) and the self-organizing map (SOM). None of the individual measurement techniques were able to describe the state of the process alone, although they provided important information about the process. By combining the data and visualizing it, an overview could be achieved. The SOM approach had two advantages over the PCA: it presented the results in terms of the original variables and enabled the analysis of nonlinear responses. However, both visualization methods could be used to describe the progress of the process and to increase the level of process understanding.     

Flexible Multibody Systems Models Using Composite Materials Components

The use of a multibody methodology to describe the large motion of complex systems that experience structural deformations enables to represent the complete system motion, the relative kinematics between the components involved, the deformation of the structural members and the inertia coupling between the large rigid body motion and the system elastodynamics. In this work, the flexible multibody dynamics formulations of complex models are extended to include elastic components made of composite materials, which may be laminated and anisotropic. The deformation of any structural member must be elastic and linear, when described in a coordinate frame fixed to one or more material points of its domain, regardless of the complexity of its geometry. To achieve the proposed flexible multibody formulation, a finite element model for each flexible body is used. For the beam composite material elements, the sections properties are found using an asymptotic procedure that involves a two-dimensional finite element analysis of their cross-section. The equations of motion of the flexible multibody system are solved using an augmented Lagrangian formulation and the accelerations and velocities are integrated in time using a multi-step multi-order integration algorithm based on the Gear method.     

Development of chemical sensors based on redox-dependent receptors: N,N'-dimethyldiazapyrenium-modified electrodes

Electrodes modified with Nafion films containing 2,7-dimethyldiazapyrenium (DAP2+) were prepared and characterized with voltammetry by themselves and in the presence of organic substrates. The large, planar, electron-poor aromatic surface in DAP2+ facilitates pi-stacking interactions with other planar aromatic molecules, particularly those that are negatively charged or electron-rich. Previous studies showed that the reduction of DAP2+ decreases the strength of these interactions, making the binding redox-dependent, and resulting in negative shifts in the E(1/2) of DAP2+/+. This study shows that the redox-dependent binding ability of DAP2+ is retained in Nafion, but the selectivity is considerably different. Most significantly, the electron-rich, neutral aromatic compounds that produced small shifts in the E(1/2) of DAP2+/+ in solution cause much larger shifts, up to -110 mV, with the modified electrodes. With indole as a substrate, Nernstian behavior is observed (-60 mV shift per log[indole]) between 10 and 0.5 mM.     

Identification and Cloning of a Pheromone-Binding Protein from the Oriental Beetle, Exomala orientalis

We have identified and cloned a pheromone-binding protein (EoriPBP) from the Japanese and American populations of the Oriental beetle, Exomala orientalis (Coleoptera: Scarabaeidae). The protein showed more than 90% amino acid identity to the previously identified pheromone-binding proteins from Popillia japonica (PjapPBP) and Anomala osakana (AosaPBP), as well as to one of the odorant-binding proteins from Phyllopertha diversa (PdivOBP1). EoriPBP has 116 amino acids, with a calculated molecular mass of 12,981 Da, pI of 4.3, and six highly conserved cysteine residues. 5-RACE amplifications led to the characterization of a signal peptide with 19 amino acids. The signal peptide showed high amino acid identity to the signal peptide for AosaPBP. Comparison of the amino acid sequences of the PBPs involved in the detection of similar ligands, i.e., monounsaturated lactones and ketone, suggests that the most variable residues among the PBPs from E. orientalis, P. japonica, and A. osakana are probably the most discriminating residues. As with the pheromone-binding protein from Bombyx mori, the residues at positions 61, 64, 71, and 82 in EoriPBP, PajpPBP, and AosaPBP, which are either valine, leucine, isoleucine, or methionine, are likely to be specificity determinants.     

Nonlinear model predictive control of biodiesel production via transesterification of used vegetable oils

The economic performance of an industrial scale semi-batch reactor for biodiesel production via transesterification of used vegetable oils is investigated by simulation using nonlinear model predictive control (NMPC) technology. The objective is to produce biodiesel compliant to the biodiesel standards at the minimum costs. A first-principle model is formulated to describe the dynamics of the reactor mixture temperature and composition. The feed oil and mixture composition are characterized using a pseudo-component approach, and the thermodynamic properties are estimated from group contribution methods. The dynamic model is used by the NMPC framework to predict the optimal control profiles, where a multiple shooting based dynamic optimization problem is solved at every sampling time. Simulation results with the economic performance of an industrial scale semi-batch reactor are presented for control configurations manipulating the methanol feed flow rate and the heat duty.     

Biosynthesis of scarab beetle pheromones

Chemical communication in scarab beetles (Coleoptera: Scarabaeidae) is achieved with a wide variety of pheromones, but one typical structure is the gamma-lactone having a long unsaturated hydrocarbon chain. Several species utilize (R, Z)-5-(-)-(oct-1-enyl)-oxacyclopentan-2-one (buibuilactone), (R, Z)-5-(-)-(dec-1-enyl)-oxacyclopentan-2-one and (S, Z)-5-(+)-(dec-1-enyl)-oxacyclopentan-2-one [(R)-japonilure and (S)-japonilure]. Using deuterated precursors, we have demonstrated that these compounds are biosynthesized from fatty acids. (9, 10-d4)-Palmitic acid, (9,10-d4)-stearic acid, (9,10-d2)-palmitoleic acid, (9,10-d2)-oleic acid, (9,10-d2)-8-hydroxypalmitoleic acid and (9,10-d2)-8-hydroxyoleic acid were readily incorporated by female Anomala cuprea into the pheromone molecules, while (Z)-(5, 6-d2)-5-dodecenoic acid and (Z)-(5,6-d2)-5-tetradecenoic acid were not. Therefore, the reaction pathway starts from saturated fatty acids, involves their desaturation, followed by 8-hydroxylation, chain shortening and cyclization. The products obtained from racemic (9,10-d2)-8-hydroxypalmitoleic acid and (9,10-d2)-8-hydroxyoleic acid were also racemic, implying that the steps following hydroxylation were not stereospecific. Perdeuterated palmitic acid was applied to disclose the mechanism of the unique hydroxylation reaction. Retention of all deuterium atoms implied that this reaction was a direct process mediated by a specific fatty acid hydroxylase, and preceding desaturation or epoxidation was not involved.