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.     

Dissociations between procedural and episodic memory: Effects of time and aging.

The issue of multiple memory systems is explored. Young and older adults (mean ages?=?20 and 71, respectively) named pictures and were tested immediately, 1, 7, or 21 days later. Episodic memory (recognition) for pictures was significantly lower in older relative to young adults and declined systematically across all retention intervals in both age groups. In contrast, procedural memory (repetition priming in picture naming) revealed no reliable age differences. In both age groups, priming declined within the first 24 hr, but unlike recognition, there was no further decrement from 1 to 21 days. There were also within-subject dissociations: The magnitude of priming was equivalent for remembered and forgotten items, and the relation between recognition and priming across intervals was nonmonotonic, revealing a reversed association. The findings were interpreted within a multiple-memory-systems framework. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Hierarchical representation of problem-solving knowledge in a frame-based process planning system

In most frame-based reasoning systems, the information being manipulated is represetned using frames, but the problem-solving knowledge that manipulates the frames is represented as production rules. One problem with this approach is that rules are not always a natrual way to represent knowledge; another is that systems containing lots of rules may suffer from problems with “exponetial blowup” in the amount of computation required. This paper describes a way to address these problems by organizing the problem-solving knowledge not as rules, but in a particular kind of frame hierarchy. the approach described in this paper has been implemented in a problem-solving system called SIPP (Semi-Intelligent Process Planner), which produces plans of action for the manufacture of metal parts. the paper gives an overview of SIPP, compares its knowledge representation and problem solving methods to approaches used in other knowledge-based systems, and describes goals for further research.     

Alkaline hydrothermal kinetics in titanate nanostructure formation

In this study, the mechanism of precursor dissolution and the influence of kinetics of dissolution on titanate nanotube formation were investigated. This comparative study explored the dissolution kinetics for the case of commercial titania powders, one composed of predominantly anatase (>95%) and the other rutile phase (>93%). These nanoparticle precursors were hydrothermally reacted in 9 mol L⁻¹ NaOH at 160 °C over a range of reaction times of between 2 and 32 h. The high surface area nanotube-form product was confirmed using X-ray diffraction, FT-Raman spectroscopy, and transmission electron microscopy. The concentration of nanotubes produced from the different precursors was established using Rietveld analysis with internal and external corundum standardization to calibrate the absolute concentrations of the samples. Interpretation of the dissolution process of the precursor materials indicated that the dissolution of anatase proceeds via a zero-order kinetic process, whereas rutile dissolution is through a second-order process. The TiO₂ nanostructure formation process and mechanism of TiO₂ precursor dissolution was confirmed by non-invasive dynamic light scattering measurements. Significant observations are that nanotube formation occurred over a broad range of hydrothermal treatment conditions and was strongly influenced by the order of precursor dissolution.     

Twin screw oil-free wet compressor for compression–absorption cycle

The performance of a twin screw compressor operating under wet (two-phase) compression conditions in an ammonia–water compression absorption heat pump cycle is investigated both theoretically and experimentally. The paper reports on the influence of the location of liquid intake or, depending what applies, injection angle and mass flow rate of the injected liquid on compressor performance. Labyrinth seals separate the oil-free process side from oil lubricated bearing housing. Labyrinth seals leakage is modelled and its impact on performance is theoretically and experimentally investigated. The need for liquid injection from the discharge side to obtain acceptable performance is discussed based on experimental results.     

Hybrid photovoltaic devices of polymer and ZnO nanofiber composites

Organic semiconductor-based photovoltaic devices offer the promise of a low-cost photovoltaic technology that could be manufactured via large-scale, roll-to-roll printing techniques. Existing organic photovoltaic devices have currently achieved solar power conversion efficiencies greater than 3%. Although encouraging, the reasons higher efficiencies have not been achieved are poor overlap between the absorption spectrum of the organic chromophores and the solar spectrum, non-ideal band alignment between the donor and acceptor species, and low charge carrier mobilities resulting from the disordered nature of organic semiconductors. To address the latter issues, we are investigating the development of nanostructured oxide/conjugated polymer composite photovoltaic (PV) devices. These composites can take advantage of the high electron mobilities attainable in oxide semiconductors and can be fabricated using low-temperature solution-based growth techniques. Additionally, the morphology of the composite can be controlled in a systematic way through control of the nanostructured oxide growth. ZnO nanostructures that are vertically aligned with respect to the substrate have been grown. Here we discuss the fabrication of such nanostructures and present results from ZnO nanofiber/poly(3-hexylthiophene) (P3HT) composite PV devices. The best performance with this cell structure produced an open circuit voltage (V_oc) of 440 mV, a short circuit current density (J_sc) of 2.2 mA/cm², a fill factor (FF) of 0.56, and a conversion efficiency (η) of 0.53%. Incorporation of a blend of P3HT and (6,6)-phenyl C₆₁ butyric acid methyl ester (PCBM) into the ZnO nanofibers produced enhanced performance with a V_oc of 475 mV, J_sc of 10.0 mA/cm², FF of 0.43, and η of 2.03%. The power efficiency is limited in these devices by the large fiber spacing and the reduced V_oc.     

High-throughput fabrication of organic nanowire devices with preferential internal alignment and improved performance

We demonstrate that arrays of nanowires of conjugated polymers can be easily produced by a simple embossing protocol, compatible with very large scale integration technology. The embossing process is shown to have the supplementary virtue to increase the internal degree of order of the nanowires, significantly enhancing their performance. This is applied to the fabrication of nanowire-based devices consisting of a liquid crystalline light-emitting polymer, of a liquid crystalline semiconducting polymer, and of an amorphous conducting polymer, illustrating the versatility and wide applicability of the method.     

Chain flexibility versus molecular entanglement response to rubbing deformation in designing poly(oxadiazole-naphthylimide)s as liquid crystal orientation layers

Four poly(oxadiazole-imide)s containing naphthalene rings, with different flexibility and molecular weight, are investigated with respect to their rheological properties to establish the optimal processing conditions from solution phase to film state for liquid crystal orientation purposes. The film uniformity and strength are determined by monitoring the flow behavior and chain entanglements. The solution rheological data are in agreement with film tensile testing, revealing that higher molecular weight favors chain entanglements and implicitly the film mechanical resistance. In order to analyze the suitability of these films as alignment layers their surface is patterned by rubbing with two types of velvet. Liquid crystal alignment of 4′-pentyl-4-biphenylcarbonitrile nematic is tested by polarized light microscopy. The resulting behavior is correlated with the polyimide malleability and characteristics of the textile fibers, namely their polarity, size, and mechanical features. The competitive effects between chain flexibility and entanglements, together with the interactions occurring between the polymer and velvet are analyzed in order to explain the surface regularity, which influences the uniformity of the liquid crystal alignment. The contrast between dark and bright states recorded on the liquid crystal cell indicates that some of these polynaphthalimides are promising candidates for liquid crystal display devices.     

Magnetic field-driven induction of ZENK in the trigeminal system of pigeons (Columba livia)

Magnetoreception remains one of the few unsolved mysteries in sensory biology. The upper beak, which is innervated by the ophthalmic branch of the trigeminal nerve (V1), has been suggested to contain magnetic sensors based on ferromagnetic structures. Recently, its existence in pigeons has been seriously challenged by studies suggesting that the previously described iron-accumulations are macrophages, not magnetosensitive nerve endings. This raised the fundamental question of whether V1 is involved in magnetoreception in pigeons at all. We exposed pigeons to either a constantly changing magnetic field (CMF), to a zero magnetic field providing no magnetic information, or to CMF conditions after V1 was cut bilaterally. Using immediate early genes as a marker of neuronal responsiveness, we report that the trigeminal brainstem nuclei of pigeons, which receive V1 input, are activated under CMF conditions and that this neuronal activation disappears if the magnetic stimuli are removed or if V1 is cut. Our data suggest that the trigeminal system in pigeons is involved in processing magnetic field information and that V1 transmits this information from currently unknown, V1-associated magnetosensors to the brain.