Estimating Distributions of Parameters in Nonlinear State Space Models with Replica Exchange Particle Marginal Metropolis–Hastings Method

Extracting latent nonlinear dynamics from observed time-series data is important for understanding a dynamic system against the background of the observed data. A state space model is a probabilistic graphical model for time-series data, which describes the probabilistic dependence between latent variables at subsequent times and between latent variables and observations. Since, in many situations, the values of the parameters in the state space model are unknown, estimating the parameters from observations is an important task. The particle marginal Metropolis–Hastings (PMMH) method is a method for estimating the marginal posterior distribution of parameters obtained by marginalization over the distribution of latent variables in the state space model. Although, in principle, we can estimate the marginal posterior distribution of parameters by iterating this method infinitely, the estimated result depends on the initial values for a finite number of times in practice. In this paper, we propose a replica exchange particle marginal Metropolis–Hastings (REPMMH) method as a method to improve this problem by combining the PMMH method with the replica exchange method. By using the proposed method, we simultaneously realize a global search at a high temperature and a local fine search at a low temperature. We evaluate the proposed method using simulated data obtained from the Izhikevich neuron model and Lévy-driven stochastic volatility model, and we show that the proposed REPMMH method improves the problem of the initial value dependence in the PMMH method, and realizes efficient sampling of parameters in the state space models compared with existing methods.     

Transesterification in polymer blends including polycarbonate at high temperatures

Miscibility of polycarbonate (PC)/poly (arylate) (PAr) was studied by differential scanning calorimetry (DSC), phase contrast microscopy with digital image analysis (DIA) system, FT-IR spectroscopy, and cloud points for the PC/PAr/methylene chloride ternary systems. PC and PAr were immiscible over the whole composition range from the thermodynamical viewpoint. However, PC/PAr is homogenized by transesterification between PC and PAr at high temperatures. There is observed a competition between phase separation due to thermodynamical factor and phase dissolution due to transesterification. The pattern of the phase separation was spinodal decomposition type and the structure was successfully analysed by DIA.     

Organoruthenium-catalyzed chemical protein synthesis to elucidate the functions of epigenetic modifications on heterochromatin factors

The application of organometallic compounds for protein science has received attention. Recently, total chemical protein synthesis using transition metal complexes has been developed to produce various proteins bearing site-specific posttranslational modifications (PTMs). However, in general, significant amounts of metal complexes were required to achieve chemical reactions of proteins bearing a large number of nucleophilic functional groups. Moreover, syntheses of medium-size proteins (>20 kDa) were plagued by time-consuming procedures due to cumbersome purification and isolation steps, which prevented access to variously decorated proteins. Here, we report a one-pot multiple peptide ligation strategy assisted by an air-tolerant organoruthenium catalyst that showed more than 50-fold activity over previous palladium complexes, leading to rapid and quantitative deprotection on a protein with a catalytic amount (20 mol%) of the metal complex even in the presence of excess thiol moieties. Utilizing the organoruthenium catalyst, heterochromatin factors above 20 kDa, such as linker histone H1.2 and heterochromatin protein 1α (HP1α), bearing site-specific PTMs including phosphorylation, ubiquitination, citrullination, and acetylation have been synthesized. The biochemical assays using synthetic proteins revealed that the citrullination at R53 in H1.2 resulted in the reduced electrostatic interaction with DNA and the reduced binding affinity to nucleosomes. Furthermore, we identified a key phosphorylation region in HP1α to control its DNA-binding ability. The ruthenium chemistry developed here will facilitate the preparation of a variety of biologically and medically significant proteins containing PTMs and non-natural amino acids.

Chemical protein synthesis assisted by an organoruthenium catalyst streamlined the production of heterochromatin factors bearing various patterns of epigenetic modifications, and their biological significance was elucidated.     

Synthesis,structure, and swelling behavior of two-component copolymer networks

A two-component copolymer network comprising polystyrene (PS) and poly(dimethylsiloxane) (PDMS) as copolymer components was prepared by cross-linking PS with telechelic PDMS with a new method. The microphase structure of the dry PS/PDMS network was found to be irregular from DSC and small angle X-ray scattering measurements. The swelling behavior was observed in three kinds of mixed solvents which were chosen so as to contrast with one another in respect of solubility of the component polymers. The observed swelling degree depended on the solvent composition in a manner peculiar to the respective mixed solvent systems. The Flory swelling equation extended to the two-component polymer network qualitatively reproduced the experimental swelling behavior.     

Reaction of an ammonium eneselenolate derived from a selenothioacetic acid S-ester with electron-deficient alkenes and alkynes

Ammonium eneselenolate 2 derived from selenothioic acid S-ester 1 was reacted with electron-deficient alkenes 4 and alkynes 9 . Ammonium eneselenolate 2 underwent Michael addition with 4 to give two types of Michael adducts, 5 and 6 . Products 6 incorporated two molecules of 4 . In contrast, the reaction of 2 with 9 took place at the selenium atom to give γ-oxo divinyl selenides 10 with high Z-stereoselectivity. During the further elaboration of the reactivity of the products derived from 2 and carbonyl compounds, unexpected reaction was found in the addition of vinylmagnesium bromide to Se-vinyl ester 3 . The spectroscopic data supported the formation of the enol form 12 of β-oxo selenothioic acid S-ester 13 . © 2004 Wiley Periodicals, Inc. Heteroatom Chem 15:187–192, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20003     

Application of benzophenones to elucidate the photochemical reaction pathways of hydrogen peroxide with dimethylsulfoxide

Benzophenone ((C₆H₅)₂CO) and decafluorobenzophenone ((C₆F₅)₂CO) were applied to elucidate the photochemical reaction pathway of hydrogen peroxide (H₂O₂) with dimethylsulfoxide (DMSO). When a solution of benzophenone in DMSO was excited with the 355 nm laser light, three transient species were observed in the time-resolved electron paramagnetic resonance spectra: benzophenone ketyl (C₆H₅)₂COH^⋅, methyl^⋅CH₃, and methylsulfinic methyl^⋅CH₂SOCH₃ radicals. However, when decafluoro-benzophenone was used with DMSO, only ketyl and methylsulfinic methyl radicals were observed under the same experimental conditions. When the reaction of benzophenone and DMSO was carried out in the presence of H₂O₂, different time profiles of^⋅CH₃ radicals were observed. In the reaction of decafluorobenzophenone-DMSO-H₂O₂, the time profiles of the radicals were not affected by the presence of H₂O₂. Thus, these results verify that^⋅CH₃ radicals are regenerated in a cyclic pathway, in which^⋅CH₃ radicals attack H₂O₂. The regeneration pathway allows us to observe f-pair polarization throughout the lifetime of^⋅CH₃ radicals, which last several microseconds, an order of magnitude longer than theT ₁ relaxation time of^⋅CH₃ radicals.     

Imaging of an Absorbing Object Embedded in a Dense Scattering Medium by Diffusing Light Topography

A new and simple imaging method for an absorbing object embedded in a dense scattering medium is proposed. The distinct characteristic is the positive usage of the diffusing light in the dense scattering medium to image the absorbing object. The principle is based on the equivalence between a probability distribution function of the path-length and a backscattered intensity distribution integrated spatially in the boundary plane between the medium and the air. The usefulness of the proposed method is experimentally confirmed for a modified pyramidal object painted black and thin tubes filled with black and red inks. The conditions under which the better image can be reconstructed are confirmed from the results of experiments and simulations. It is finally shown that our proposed method is capable of imaging the map of blood vessels distributed under the skin layers.     

Preparation of Cu/SiO2 Catalyst by Solution Exchange of Wet Silica Gel

Structural formation process of Ni/SiO₂ and Cu/SiO₂ catalysts prepared by solution exchange of wet silica gel was investigated. Microstructures of Cu/SiO₂ and Ni/SiO₂ were quite different from each other. In the case of Cu/SiO₂, Cu particles with diameter of ca. 3–5 nm dispersed homogeneously at less Cu content, and the particle size of Cu as well as pore size of silica gel support increased with increasing Cu content. In the Ni/SiO₂, the Ni particles with diameter of ca. 6–10 nm gathered densely to form aggregates in silica matrix resulting in sea-island structure, whereas the size of Ni particle slightly increased with increasing Ni content. The difference in the structure of the metal-silica composites is probably caused by the difference in interaction between silica gel network and metal ions during drying and heating processes.