State-selective frustration as a key driver of allosteric pluripotency

Allosteric pluripotency arises when an allosteric effector switches from agonist to antagonist depending on the experimental conditions. For example, the Rp-cAMPS ligand of Protein Kinase A (PKA) switches from agonist to antagonist as the MgATP concentration increases and/or the kinase substrate affinity or concentration decreases. Understanding allosteric pluripotency is essential to design effective allosteric therapeutics with minimal side effects. Allosteric pluripotency of PKA arises from divergent allosteric responses of two homologous tandem cAMP-binding domains, resulting in a free energy landscape for the Rp-cAMPS-bound PKA regulatory subunit R1a in which the ground state is kinase inhibition-incompetent and the kinase inhibition-competent state is excited. The magnitude of the free energy difference between the ground non-inhibitory and excited inhibitory states (ΔG_R,Gap) relative to the effective free energy of R1a binding to the catalytic subunit of PKA (ΔG_R:C) dictates whether the antagonism-to-agonism switch occurs. However, the key drivers of ΔG_R,Gap are not fully understood. Here, by analyzing an R1a mutant that selectively silences allosteric pluripotency, we show that a major determinant of ΔG_R,Gap unexpectedly arises from state-selective frustration in the ground inhibition-incompetent state of Rp-cAMPS-bound R1a. Such frustration is caused by steric clashes between the phosphate-binding cassette and the helices preceding the lid, which interact with the phosphate and base of Rp-cAMPS, respectively. These clashes are absent in the excited inhibitory state, thus reducing the ΔG_R,Gap to values comparable to ΔG_R:C, as needed for allosteric pluripotency to occur. The resulting model of allosteric pluripotency is anticipated to assist the design of effective allosteric modulators.

The Rp-cAMPS ligand of protein kinase A switches from agonist to antagonist depending on metabolite and proteomic contexts. We show that the state-selective frustration is a key driver of this allosteric pluripotency phenomenon.     

Portrait Segmentation Using Ensemble of Heterogeneous Deep-Learning Models

Image segmentation plays a central role in a broad range of applications, such as medical image analysis, autonomous vehicles, video surveillance and augmented reality. Portrait segmentation, which is a subset of semantic image segmentation, is widely used as a preprocessing step in multiple applications such as security systems, entertainment applications, video conferences, etc. A substantial amount of deep learning-based portrait segmentation approaches have been developed, since the performance and accuracy of semantic image segmentation have improved significantly due to the recent introduction of deep learning technology. However, these approaches are limited to a single portrait segmentation model. In this paper, we propose a novel approach using an ensemble method by combining multiple heterogeneous deep-learning based portrait segmentation models to improve the segmentation performance. The Two-Models ensemble and Three-Models ensemble, using a simple soft voting method and weighted soft voting method, were experimented. Intersection over Union (IoU) metric, IoU standard deviation and false prediction rate were used to evaluate the performance. Cost efficiency was calculated to analyze the efficiency of segmentation. The experiment results show that the proposed ensemble approach can perform with higher accuracy and lower errors than single deep-learning-based portrait segmentation models. The results also show that the ensemble of deep-learning models typically increases the use of memory and computing power, although it also shows that the ensemble of deep-learning models can perform more efficiently than a single model with higher accuracy using less memory and less computing power.     

Morrey regularity of solutions to quasilinear elliptic equations over Reifenberg flat domains

We derive global gradient estimates in Morrey spaces for the weak solutions to discontinuous quasilinear elliptic equations related to important variational problems arising in models of linearly elastic laminates and composite materials. The principal coefficients of the quasilinear operator are supposed to be merely measurable in one variable and to have small-BMO seminorms in the remaining orthogonal directions, and the nonlinear terms are subject to controlled growth conditions with respect to the unknown function and its gradient. The boundary of the domain considered is Reifenberg flat which includes boundaries with rough fractal structure. As outgrowth of the main result we get global Hölder continuity of the weak solution with exact value of the corresponding exponent.     

Dependence of propagation loss on etching depth in Al0.3Ga0.7As/GaAs/Al0.3Ga0.7As strip-loaded type waveguides

Al_0.3Ga_0.7As/GaAs/Al_0.3Ga_0.7As strip-loaded waveguides were fabricated using a broad-beam electron cyclotron resonance (ECR) ion source. It was found that a very smooth etching profile can be obtained by ECR ion etching and the etching rate of Al_0.3Ga_0.7As is 70 nm min^-1. The propagation losses of strip-loaded type III–V compound semiconductor waveguides with various etching depths were studied by the Fabry-Perot cavity method. It was observed that the reflectance at the cleavage increases slightly with etching depth for TE polarization. The propagation loss is measured as 1.5 dB cm^-1 for etching depth of 0.7 m, less than 1 dB cm^-1 for 0.8 m, and 3.5 dB cm^-1 for 1.1 m.     

On vanishing of characteristic numbers in Poincaré complexes

Let be the evaluation subgroup as defined by Gottlieb. Assume the Hurewicz map is non-trivial and is a field. We will prove: if is a Poincaré complex oriented in -coefficient, all the characteristic numbers of in -coefficient vanish. Similarly, if and is a -Poincaré complex, then all the mod Wu numbers vanish. We will also show that the existence of a non-trivial derivation on with some suitable conditions implies vanishing of mod Wu numbers.

     

The identification of irradiated seasoned filefish (Thamnaconus modestus) by different analytical methods

Dried seasoned filefish (Thamnaconus modestus) was irradiated at 0–10 kGy and the identification of irradiation treatment was investigated by analyzing the characteristics of thermoluminescence (TL), hydrocarbon (HC), and 2-alkylacyclobutanone (2-ACB). The TL (TL₁), glow curve of the irradiated samples peaked at approximately 150 °C with high intensity, but that of the non-irradiated samples peaked at about 300 °C with little intensity, thus making it possible to discriminate between irradiated and non-irradiated samples. Moreover, TL ratio (TL₁/TL₂), through normalization steps, enhanced the reliability of the TL₁ results. Six kinds of HCs and three kinds of 2-ACBs quantitatively determined for the samples linearly increased in proportion to irradiation doses. In particular, two HCs like 1-hexadecane and 1,7-hexadecadine, and three ACBs, such as 2-dodecylcyclobutanone, 2-(5′-tetradeceyl)cyclobutanone, and 2-tetradecylcyclobutanone, were identified only in the irradiated samples as radiation-induced markers.     

Triterpenoid saponins from the roots of Sophora koreensis

From the roots of Sophora koreensis (Fabaceae), three new oleanene-type triterpene glycosides, echinosophorosides A(1) (1) and B (2), and acetyl-subproside II (5), were isolated as their methyl esters, together with the four known ones sophoraflavoside I, kudzusaponin SA(3), subproside II, and azukisaponin V. The structures of the new saponins were elucidated to be 3-O-alpha-L-rhamnopyranosyl(1-->2)-alpha-L-arabinopyranosyl(1-->2)-beta-D-glucuronopyranosyl kudzusapogenol A 22-O-alpha-L-arabinopyranoside (1), 3-O-alpha-L-rhamnopyranosyl(1-->2)-alpha-L-arabinopyranosyl-(1-->2)-beta-D-glucuronopyranosyl abrisapogenol C 22-O-alpha-L-arabinopyranoside (2), and 3-O-alpha-L-rhamnopyranosyl(1-->2)-alpha-L-arabinopyranosyl(1-->2)-beta-D-glucuronopyranosyl kudzusapogenol A 22-O-acetate (5), respectively. It is noteworthy that two arabinopyranosyl moieties in the same molecule, echinosophoroside B (2), have different conformations. The conformation of the arabinopyranosyl moiety existing in the trisaccharide moiety was determined to be (1)C(4), whereas that of the arabinopyranosyl unit at C-22 was identified as (4)C(1).     

Solvent effects on the nπ* transition of pyrimidine in aqueous solution

A hybrid quantum mechanical and molecular mechanical potential is used in Monte Carlo simulations to examine the solvent effects on the electronic excitation energy for the n→π* transition of pyrimidine in aqueous solution. In the present study, the pyrimidine molecule is described by the semi-empirical AM1 model, while the solvent molecules are treated classically. Two sets of calculations are performed: the first involves the use of the pairwise three-point charge TIP3P model for water, and the second computation employs a polarizable many-body potential for the solvent. The latter calculation takes into account the effect of solvent polarization following the solute electronic excitation, and makes a correction to the energies determined using pairwise potentials, which neglects such fast polarization effects and overestimates the solute-solvent interactions on the Franck-Condon excited states. Our simulation studies of pyrimidine in water indicate that the solvent charge redistribution following the solute electronic excitation makes modest corrections (about −130␣cm⁻¹) to the energy predicted by using pairwise potentials. Specific hydrogen bonding interactions between pyrimidine and water are important for the prediction of solvatochromic shifts for pyrimidine. The computed n→π* blue shift is 2275±110 cm⁻¹, which may be compared with the experimental value (2700 cm⁻¹) from isooctane to water. Received: 14 January 1997 / Accepted: 21 February 1997