New methods to measure residues coevolution in proteins

<p>Abstract</p> <p>Background</p> <p>The covariation of two sites in a protein is often used as the degree of their coevolution. To quantify the covariation many methods have been developed and most of them are based on residues position-specific frequencies by using the mutual information (MI) model.</p> <p>Results</p> <p>In the paper, we proposed several new measures to incorporate new biological constraints in quantifying the covariation. The first measure is the mutual information with the amino acid background distribution (MIB), which incorporates the amino acid background distribution into the marginal distribution of the MI model. The modification is made to remove the effect of amino acid evolutionary pressure in measuring covariation. The second measure is the mutual information of residues physicochemical properties (MIP), which is used to measure the covariation of physicochemical properties of two sites. The third measure called MIBP is proposed by applying residues physicochemical properties into the MIB model. Moreover, scores of our new measures are applied to a robust indicator <it>conn(k) </it>in finding the covariation signal of each site.</p> <p>Conclusions</p> <p>We find that incorporating amino acid background distribution is effective in removing the effect of evolutionary pressure of amino acids. Thus the MIB measure describes more biological background information for the coevolution of residues. Besides, our analysis also reveals that the covariation of physicochemical properties is a new aspect of coevolution information.</p

Perceptual Quality Assessment of NeRF and Neural View Synthesis Methods for Front-Facing Views

Neural view synthesis (NVS) is one of the most successful techniques for synthesizing free viewpoint videos, capable of achieving high fidelity from only a sparse set of captured images. This success has led to many variants of the techniques, each evaluated on a set of test views typically using image quality metrics such as PSNR, SSIM, or LPIPS. There has been a lack of research on how NVS methods perform with respect to perceived video quality. We present the first study on perceptual evaluation of NVS and NeRF variants. For this study, we collected two datasets of scenes captured in a controlled lab environment as well as in-the-wild. In contrast to existing datasets, these scenes come with reference video sequences, allowing us to test for temporal artifacts and subtle distortions that are easily overlooked when viewing only static images. We measured the quality of videos synthesized by several NVS methods in a well-controlled perceptual quality assessment experiment as well as with many existing state-of-the-art image/video quality metrics. We present a detailed analysis of the results and recommendations for dataset and metric selection for NVS evaluation

Isolation and Characterization of Minipig Perivascular Stem Cells for Bone Tissue Engineering

Human subcutaneous adipose tissue has been recognized as a rich source of tissue resident mesenchymal stem/stromal cells (MSC) in recent years. The current study was designed to sort the minipig (mp) perivascular stem cells (PSCs) and investigate the osteogenic potential. Purification of human PSCs was achieved via fluorescence-activated cell sorting (FACS) from human liposuction samples [cluster of differentiation (CD)45-CD34-CD146+ perithelial cells and CD45-CD34+CD146- adventitial cells]. Subsequently, PSCs were isolated from mp adipose tissue samples (n=9), characterized and, using purified mpPSCs (obtained by FACS, which is used in human PSC purification), the mpPSC osteogenic and adipogenic potential was evaluated by Alizarin Red S and Oil Red O staining in vitro, respectively. The cell morphometry was observed following cell isolation and culture, and hematoxylin and eosin staining was performed to identify the fat tissue structure and vascular distribution. Osteogenic and adipogenic differentiation-associated gene expression levels were analyzed by reverse transcription-quantitative polymerase chain reaction. The results demonstrated that the same antigens used for human PSC identification and isolation were working in mp tissue (CD45, CD146 and CD34). The two cell groups: CD45-CD34-CD146+ pericytes and CD45-CD34+CD146- adventitial cells were successfully isolated from the subcutaneous fat in the posterior neck of mps, mpPSCs accounted for 8.6% of the stromal vascular fraction (SVF) with 1.4% pericytes and 7.2% adventitial cells. mpPSCs demonstrated characteristics of MSCs, including cell surface marker expression, colony forming unit-fibroblast inclusion, and the stronger osteogenic and adipogenic differentiation potential than that of the non-selected vascular stromal cells. The mRNA expression levels of osteocalcin, collagen, type I, α1 and peroxisome proliferator-activated receptor-γ in the mpPSCs group were significantly higher than those of the unsorted pSVF group (P\u3c0.05). Thus, the current study successfully isolated and cultured CD146+ and CD34+ cell populations from mp tissues, characterized the cells\u27 PSC-like phenotype and identified their distinctly osteogenic and adipogenic potential. © Spandidos Publications. All rights reserved

Complex polymer architectures through free-radical polymerization of multivinyl monomers

The construction of complex polymer architectures with well-defined topology, composition and functionality has been extensively explored as the molecular basis for the development of modern polymer materials. The unique reaction kinetics of free-radical polymerization leads to the concurrent formation of crosslinks between polymer chains and rings within an individual chain and, thus, free-radical (co)polymerization of multivinyl monomers provides a facile method to manipulate chain topology and functionality. Regulating the relative contribution of these intermolecular and intramolecular chain-propagation reactions is the key to the construction of architecturally complex polymers. This can be achieved through the design of new monomers or by spatially or kinetically controlling crosslinking reactions. These mechanisms enable the synthesis of various polymer architectures, including linear, cyclized, branched and star polymer chains, as well as crosslinked networks. In this Review, we highlight some of the contemporary experimental strategies to prepare complex polymer architectures using radical polymerization of multivinyl monomers. We also examine the recent development of characterization techniques for sub-chain connections in such complex macromolecules. Finally, we discuss how these crosslinking reactions have been engineered to generate advanced polymer materials for use in a variety of biomedical applications