Dirichlet Priors for MAP Inference of Protein Conformation Abundances from SAXS

Estimation of mixture coefficients of protein conformations in solution find applications in understanding protein behavior. We describe a method for maximum a posteriori (MAP) estimation of the mixture coefficients of ensemble of conformations in a protein mixture solution using measured small angle X-ray scattering (SAXS) intensities. The proposed method builds upon a model for the measurements of crystallographically determined conformations. Assuming that a priori information on the protein mixture is available, and that priori information follows a Dirichlet distribution, we develop a method to estimate the relative abundances with MAP estimator. The Dirichlet distribution depends on concentration parameters which may not be known in practice and thus need to be estimated. To estimate these unknown concentration parameters we developed an expectation-maximization (EM) method. Adenylate kinase (ADK) protein was selected as the test bed due to its known conformations Beckstein et al. (Journal of Molecular Biology, 394(1), 160 1). Known conformations are assumed to form the full vector bases that span the measurement space. In Monte Carlo simulations, mixture coefficient estimation performances of MAP and maximum likelihood (ML) (which assumes a uniform prior on the mixture coefficients) estimators are compared. MAP estimators using known and unknown concentration parameters are also compared in terms of estimation performances. The results show that prior knowledge improves estimation accuracy, but performance is sensitive to perturbations in the Dirichlet distribution’s concentration parameters. Moreover, the estimation method based on EM algorithm shows comparable results to approximately known prior parameters.     

Genetic Algorithm for the Multiple-Query Optimization Problem

Producing answers to a set of queries with common tasks efficiently is known as the multiple-query optimization (MQO) problem. Each query can have several alternative evaluation plans, each with a different set of tasks. Therefore, the goal of MQO is to choose the right set of plans for queries which minimizes the total execution time by performing common tasks only once. Since MQO is an NP-hard problem, several, mostly heuristics based, solutions have been proposed for solving it. To the best of our knowledge, this correspondence is the first attempt to solve MQO using an evolutionary technique, genetic algorithms     

Superresolution video reconstruction with arbitrary samplinglattices and nonzero aperture time

Printing from an NTSC source and conversion of NTSC source material to high-definition television (HDTV) format are some of the applications that motivate superresolution (SR) image and video reconstruction from low-resolution (LR) and possibly blurred sources. Existing methods for SR image reconstruction are limited by the assumptions that the input LR images are sampled progressively, and that the aperture time of the camera is zero, thus ignoring the motion blur occurring during the aperture time. Because of the observed adverse effects of these assumptions for many common video sources, this paper proposes (i) a complete model of video acquisition with an arbitrary input sampling lattice and a nonzero aperture time, and (ii) an algorithm based on this model using the theory of projections onto convex sets to reconstruct SR still images or video from an LR time sequence of images. Experimental results with real video are provided, which clearly demonstrate that a significant increase in the image resolution can be achieved by taking the motion blurring into account especially when there exists large interframe motion.     

Review and comparative evaluation of symbolic dynamic filtering for detection of anomaly patterns

Symbolic dynamic filtering (SDF) has been recently reported in literature as a pattern recognition tool for early detection of anomalies (i.e., deviations from the nominal behavior) in complex dynamical systems. This paper presents a review of SDF and its performance evaluation relative to other classes of pattern recognition tools, such as Bayesian Filters and Artificial Neural Networks, from the perspectives of: (i) anomaly detection capability, (ii) decision making for failure mitigation and (iii) computational efficiency. The evaluation is based on analysis of time series data generated from a nonlinear active electronic system. This work has been supported in part by the U.S. Army Research Laboratory and the U.S. Army Research Office under Grant No. W911NF-07-1-0376, by the U.S. Office of Naval Research under Grant No. N00014-08-1-380, and by NASA under Cooperative Agreement No. NNX07AK49A.     

Subsurface radar signal deconvolution

We present two methods of signal deconvolution for systems whose impulse response (wavelet function) can be explicitly determined, and where the goal is to locate short impulses in the presence of strong, reverberation-like interferences.The first method, which we call algebraic deconvolution, differs from other known techniques in two ways: first of all, explicit use of the wavelet function provides more powerful a priori knowledge than the autocorrelation or the power spectrum. Secondly, this method permits to flexibly trade off noise versus resolution.In the second method presented here, we use an analytical model (synthetic wavelet) of the system impulse response to determine an inverse filter.These methods have been developed for video pulse radar signals, and encouraging early results have been obtained.     

Application of antimicrobial ice for extending shelf life of fish

In this study, we investigated whether wild-thyme (Thymus serpyllum) hydrosol had a preserving effect against spoilage of freshwater fish. Sensorial characteristics, chemical freshness indicator contents, and microbial counts (total aerobes, psychrotrophics, Enterobacteriaceae, fecal coliform bacteria, Aeromonas spp., and Pseudomonas spp.) of whole ungutted and gutted Transcaucasian barb (Capoeta capoeta capoeta Guldenstaedt, 1772) stored on ice produced from wild-thyme hydrosol and tap water at 4 degrees C for 20 days were compared. The results did not reveal any significant (P > 0.05) differences in the microbial counts, sensorial characteristics, pH, and total volatile basic nitrogen values between gutted and ungutted groups. Sensory evaluation and microbiological and chemical analyses indicated that the storage of the fish on ice produced from wild-thyme hydrosol had a significant increase in shelf life by at least 15 to 20 days.     

Polyamorphism in Aluminum Nitride: A First Principles Molecular Dynamics Study

The high‐pressure behavior of amorphous aluminum nitride is investigated for the first time by means of ab initio molecular dynamics simulations. It is found to undergo two successive first‐order phase transformations with the application of pressure. The first one is a polyamorphic phase transition in which the low‐density amorphous phase transforms into a high‐density amorphous phase having an average coordination number of about 4.6. The high‐density amorphous structure transforms back to a low‐coordinated amorphous network upon pressure release but its density is higher than that of the original low‐density amorphous phase. The second phase change is the crystallization of the high‐density amorphous state into a rocksalt structure. A careful analysis suggests that the hexagonal‐like nanoclusters presented in amorphous aluminum nitride prevent the formation of a very dense amorphous phase (about sixfold coordinated) during the first phase transition and they act as a nucleation center for the crystallization process.     

Effect of Dynamic Compaction on the Retention of Tetragonal Zirconia and Mechanical Properties of Alumina/Zirconia Composites

Dynamic consolidation techniques were employed to investigate the retention of tetragonal zirconia and degree of consolidation in alumina/zirconia powder compacts. Heating the specimens prior to explosive shock compaction increased the tetragonal-phase retention significantly. Low shock pressures yielded no macrocracking, although final densities were low (60% to 70% of the theoretical density). Heat treatment following dynamic consolidation enhanced the retention of the tetragonal zirconia polymorph regardless of the shock pressure employed. Compact densities were increased to over 90% of theoretical at relatively low sintering temperatures (1300°C). Hardness, toughness, and Young's modulus of the compacts were comparable to those achieved in composites that were synthesized using more conventional techniques. Dynamic compaction offers an alternative method for the fabrication of zirconia-toughened alumina ceramics.     

Synthesis and characterization of a Zr‐containing silicate‐based epoxy‐functional polymer nanocomposite system

As a continuation of efforts to explore the potential of certain types of polymer nanocomposites to be successful candidates as dental restoration/adhesion materials, a Zr‐containing and organically modified silicate‐based material system with epoxy functionality was prepared by use of a sol–gel synthesis method, and UV light‐ and visible light (VL)‐curing processes. Comparative influences of the synthesis and processing parameters on the mechanical, thermal, and microstructural/nanostructural properties of the system were detailed. Zr‐containing species proved to more effectively catalyze the epoxy polymerization/crosslinking reactions than those containing Ti. Incorporation of Zr into the nanocomposite network led to significantly advanced mechanical properties. An elastic (Young's) modulus value of 23 MPa was achieved. The system with relatively high Zr content was successfully obtained, which also had higher thermal stability. Overall observations and results suggested that Zr content, and the UV light‐ or VL‐curing process could be capitalized on to modify the structure, and to improve the final properties of these material systems, which indicated a prospective opportunity for this material system to be utilized in dental restoration/adhesion applications. POLYM. ENG. SCI., 55:792–798, 2015. © 2014 Society of Plastics Engineers