ProteoFind : A script for finding proteins that are suitable for chemical synthesis

ProteoFind is a computational script for finding proteins that are suitable for fragment ligation-based chemical synthesis. This paper describes the development and case studies of ProteoFind, which searches protein lists obtained from the UniProt website. Its application to visualize areas covered by several one-pot three-fragment ligation methods is also discussed. The results demonstrate that ProteoFind not only saves time when searching for synthetic target proteins, but also proposes many candidate proteins from among which biomedically interesting proteins could be found. It also enables clarification of the features of ligation methods by comparing the areas to which each ligation reaction is accessible

Isotropization of Quaternion-Neural-Network-Based PolSAR Adaptive Land Classification in Poincare-Sphere Parameter Space

Quaternion neural networks (QNNs) achieve high accuracy in polarimetric synthetic aperture radar classification for various observation data by working in Poincare-sphere-parameter space. The high performance arises from the good generalization characteristics realized by a QNN as 3-D rotation as well as amplification/attenuation, which is in good consistency with the isotropy in the polarization-state representation it deals with. However, there are still two anisotropic factors so far which lead to a classification capability degraded from its ideal performance. In this letter, we propose an isotropic variation vector and an isotropic activation function to improve the classification ability. Experiments demonstrate the enhancement of the QNN ability

Electromagnetic and thermal responses in topological matter: topological terms, quantum anomalies and D-branes

We discuss the thermal (or gravitational) responses in topological superconductors and in topological phases in general. Such thermal responses (as well as electromagnetic responses for conserved charge) provide a definition of topological insulators and superconductors beyond the single-particle picture. In two-dimensional topological phases, the Str\v{e}da formula for the electric Hall conductivity is generalized to the thermal Hall conductivity. Applying this formula to the Majorana surface states of three-dimensional topological superconductors predicts cross-correlated responses between the angular momentum and thermal polarization (entropy polarization). We also discuss a use of D-branes in string theory as a systematic tool to derive all such topological terms and topological responses. In particular, we relate the $\mathbb{Z}_2$ index of topological insulators introduced by Kane and Mele (and its generalization to other symmetry classes and to arbitrary dimensions) to the K-theory charge of non-BPS D-branes, and vice versa. We thus establish a link between the stability of non-BPS D-branes and the topological stability of topological insulators.Comment: 16 pages, 2 figures; Submitted to a topical issue of the Comptes Rendus de l Academie des Sciences (CRAS

Resin-Bound Crypto-Thioester for Native Chemical Ligation

Resin-bound N–sulfanylethylanilide (SEAlide) peptide was found to function as a crypto-thioester peptide. Exposure of the peptide resin to an aqueous solution under neutral conditions in the presence of thiols affords thioesters without accompanying racemization of C-terminal amino acids. Furthermore, the resin-bound SEAlide peptides react with N-terminal cysteinyl peptides in the absence of phosphate salts to afford ligated products, whereas soluble SEAlide peptides do not. This unexpected difference in reactivity of the SEAlide peptides allows for a one-pot/three-fragment ligation using resin-bound and unbound peptides

Degree of Polarization-Based Data Filter for Fully Polarimetric Synthetic Aperture Radar

This paper proposes a novel data filtering algorithm for fully polarimetric synthetic aperture radar (PolSAR) based on the degree of polarization (DoP) information. First, we define the homogeneity degree and polarization independence degree using the DoP information, and propose a feature plane to characterize the target feature. Second, employing the feature plane, we categorize the targets into three types and assign specific filtering policy for each type to estimate the optimal filtering window sizes. Finally, the $T$ -matrices of fully PolSAR data are filtered using the windows with estimated optimal sizes. Compared with boxcar filter, refined Lee filter, scattering model-based filter, and improved sigma filter in processing ALOS2-PALSAR2 data, the proposed DoP-based algorithm presents the best filtering performance