Influence of RNA Strand Rigidity on Polyion Complex Formation with Block Catiomers

Polyion complexes (b‐PICs) are prepared by mixing single‐ or double‐stranded oligo RNA (aniomer) with poly(ethylene glycol)‐b‐poly(l ‐lysine) (PEG‐PLL) (block catiomer) to clarify the effect of aniomer chain rigidity on association behaviors at varying concentrations. Here, a 21‐mer single‐stranded RNA (ssRNA) (persistence length: 1.0 nm) and a 21‐mer double‐stranded RNA (small interfering RNA, siRNA) (persistence length: 62 nm) are compared. Both oligo RNAs form a minimal charge‐neutralized ionomer pair with a single PEG‐PLL chain, termed unit b‐PIC (uPIC), at low concentrations (<≈0.01 mg mL⁻¹). Above the critical association concentration (≈0.01 mg mL⁻¹), ssRNA b‐PICs form secondary associates, PIC micelles, with sizes up to 30–70 nm, while no such multimolecular assembly is observed for siRNA b‐PICs. The entropy gain associated with the formation of a segregated PIC phase in the multimolecular PIC micelles may not be large enough for rigid siRNA strands to compensate with appreciably high steric repulsion derived from PEG chains. Chain rigidity appears to be a critical parameter in polyion complex association.

     

A non-negative matrix factorization model based on the zero-inflated Tweedie distribution

Non-negative matrix factorization (NMF) is a technique of multivariate analysis used to approximate a given matrix containing non-negative data using two non-negative factor matrices that has been applied to a number of fields. However, when a matrix containing non-negative data has many zeroes, NMF encounters an approximation difficulty. This zero-inflated situation occurs often when a data matrix is given as count data, and becomes more challenging with matrices of increasing size. To solve this problem, we propose a new NMF model for zero-inflated non-negative matrices. Our model is based on the zero-inflated Tweedie distribution. The Tweedie distribution is a generalization of the normal, the Poisson, and the gamma distributions, and differs from each of the other distributions in the degree of robustness of its estimated parameters. In this paper, we show through numerical examples that the proposed model is superior to the basic NMF model in terms of approximation of zero-inflated data. Furthermore, we show the differences between the estimated basis vectors found using the basic and the proposed NMF models for \(\beta \) divergence by applying it to real purchasing data.     

Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover

We propose a conformational search method to find a global minimum energy structure for protein systems. The simulated annealing is a powerful method for local conformational search. On the other hand, the genetic crossover can search the global conformational space. Our method incorporates these attractive features of the simulated annealing and genetic crossover. In the previous works, we have been using the Monte Carlo algorithm for simulated annealing. In the present work, we use the molecular dynamics algorithm instead. To examine the effectiveness of our method, we compared our results with those of the normal simulated annealing molecular dynamics simulations by using an α-helical miniprotein. We used genetic two-point crossover here. The conformations, which have lower energy than those obtained from the conventional simulated annealing, were obtained.     

Selective photoinduced energy transfer from a thiophene rotaxane to acceptor

An energy transfer process was investigated using cyclodextrin-oligothiophene rotaxanes (2T-[2]rotaxane). The excited energy of 2T-[2]rotaxane is transferred to the sexithiophene derivative which is included in the cavity of β-CD stoppers of 2T-[2]rotaxane.     

Abnormal phospholipids distribution in the prefrontal cortex from a patient with schizophrenia revealed by matrix-assisted laser desorption/ionization imaging mass spectrometry

Schizophrenia is one of the major psychiatric disorders, and lipids have focused on the important roles in this disorder. In fact, lipids related to various functions in the brain. Previous studies have indicated that phospholipids, particularly ones containing polyunsaturated fatty acyl residues, are deficient in postmortem brains from patients with schizophrenia. However, due to the difficulties in handling human postmortem brains, particularly the large size and complex structures of the human brain, there is little agreement regarding the qualitative and quantitative abnormalities of phospholipids in brains from patients with schizophrenia, particularly if corresponding brain regions are not used. In this study, to overcome these problems, we employed matrix-assisted laser desorption/ionization imaging mass spectrometry (IMS), enabling direct microregion analysis of phospholipids in the postmortem brain of a patient with schizophrenia via brain sections prepared on glass slides. With integration of traditional histochemical examination, we could analyze regions of interest in the brain at the micrometric level. We found abnormal phospholipid distributions within internal brain structures, namely, the frontal cortex and occipital cortex. IMS revealed abnormal distributions of phosphatidylcholine molecular species particularly in the cortical layer of frontal cortex region. In addition, the combined use of liquid chromatography/electrospray ionization tandem mass spectrometry strengthened the capability for identification of numerous lipid molecular species. Our results are expected to further elucidate various metabolic processes in the neural system.     

Isoreticular expansion of metal-organic frameworks with triangular and square building units and the lowest calculated density for porous crystals

The concept and occurrence of isoreticular (same topology) series of metal-organic frameworks (MOFs) is reviewed. We describe the preparation, characterization, and crystal structures of three new MOFs that are isoreticular expansions of known materials with the tbo (Cu(3)(4,4',4'-(benzene-1,3,5-triyl-tris(benzene-4,1-diyl))tribenzoate)(2), MOF-399) and pto topologies (Cu(3)(4,4',4'-(benzene-1,3,5-triyl-tribenzoate)(2), MOF-143; Cu(3)(4,4',4'-(triazine-2,4,6-triyl-tris(benzene-4,1-diyl))tribenzoate)(2), MOF-388). One of these materials (MOF-399) has a unit cell volume 17 times larger than that of the first reported material isoreticular to it, and has the highest porosity (94%) and lowest density (0.126 g cm(-3)) of any MOFs reported to date.     

Flow pattern,void fraction and pressure drop of refrigerant two-phase flow in a horizontal pipe—II: Analysis of frictional pressure drop

Two-phase flow in horizontal pipe was analyzed with simplified models for annular and stratified flow. The velocity profiles for the liquid and gas phase were described with the Prandtl mixing length. From this analysis, the frictional pressure drop was calculated with the modified Baker map for flow pattern transition. The intermediate region, i.e. wavy flow, was interpolated between annular and stratified flow. Comparison of this analysis with existing experimental data of refrigerants showed good agreement.     

Energy transfer between rhodamine-6G and 3,3′-diethylthiacarbocyanine iodide enhanced in the premicellar region

The energy transfer between rhodamine-6G and 3,3′-diethylthiacarbocyanine iodide was studied in aqueous solutions of sodium lauryl sulfate. A highly enhanced energy transfer was observed at very low dye concentrations in the premicellar region. This effect can be explained in terms of the formation of dye-rich mixed micelles.     

Photodissociation of molecular beams of halogenated hydrocarbons at 193 nm

Molecular beams of halogenated hydrocarbons containing chlorine and bromine atoms were photodissociated using an excimer laser at 193 nm. Molecules photodissociated were HCCBr, HCCCH₂Br, HCCCH₂Cl, CH₃Cl, C₂H₅Cl and i-C₃H₇Cl. The time-of-flight distributions of the photofragments were measured in order to study the primary processes and the dissociation dynamics. Generalizations consistent with the data are that atomic products (RX → R + X) result from direct dissociation of the CX repulsive singlet state, molecular elimination (RX → R′ + HX) is a result of a crossover to the ground state and triplet states are involved in the photodissociation of alkyne compounds.