Visual-Preserving Mesh Repair.

Mesh repair is a long-standing challenge in computer graphics and related fields. Converting defective meshes into watertight manifold meshes can greatly benefit downstream applications such as geometric processing, simulation, fabrication, learning, and synthesis. In this work, by assuming the model is visually correct, we first introduce three visual measures for visibility, orientation, and openness, based on ray-tracing. We then present a novel mesh repair framework incorporating visual measures with several critical steps, i.e., open surface closing, face reorientation, and global optimization, to effectively repair meshes with defects (e.g., gaps, holes, self-intersections, degenerate elements, and inconsistent orientations) and preserve visual appearances. Our method reduces unnecessary mesh complexity without compromising geometric accuracy or visual quality while preserving input attributes such as UV coordinates for rendering. We evaluate our approach on hundreds of models randomly selected from ShapeNet and Thingi10K, demonstrating its effectiveness and robustness compared to existing approaches.

Gene Repair of iPSC Line with GARS (G294R) Mutation of CMT2D Disease by CRISPR/Cas9.

OBJECTIVE: Charcot-Marie-Tooth disease (CMT) severely affects patient activity, and may cause disability. However, no clinical treatment is available to reverse the disease course. The combination of CRISPR/Cas9 and iPSCs may have therapeutic potential against nervous diseases, such as CMT. METHODS: In the present study, the skin fibroblasts of CMT type 2D (CMT2D) patients with the c.880G>A heterozygous nucleotide mutation in the GARS gene were reprogrammed into iPSCs using three plasmids (pCXLE-hSK, pCXLE-hUL and pCXLE-hOCT3/4-shp5-F). Then, CRISPR/Cas9 technology was used to repair the mutated gene sites at the iPSC level. RESULTS: An iPSC line derived from the GARS (G294R) family with fibular atrophy was successfully induced, and the mutated gene loci were repaired at the iPSC level using CRISPR/Cas9 technology. These findings lay the foundation for future research on drug screening and cell therapy. CONCLUSION: iPSCs can differentiate into different cell types, and originate from autologous cells. Therefore, they are promising for the development of autologous cell therapies for degenerative diseases. The combination of CRISPR/Cas9 and iPSCs may open a new avenue for the treatment of nervous diseases, such as CMT.

OctSurf: Efficient hierarchical voxel-based molecular surface representation for protein-ligand affinity prediction.

Voxel-based 3D convolutional neural networks (CNNs) have been applied to predict protein-ligand binding affinity. However, the memory usage and computation cost of these voxel-based approaches increase cubically with respect to spatial resolution and sometimes make volumetric CNNs intractable at higher resolutions. Therefore, it is necessary to develop memory-efficient alternatives that can accelerate the convolutional operation on 3D volumetric representations of the protein-ligand interaction. In this study, we implement a novel volumetric representation, OctSurf, to characterize the 3D molecular surface of protein binding pockets and bound ligands. The OctSurf surface representation is built based on the octree data structure, which has been widely used in computer graphics to efficiently represent and store 3D object data. Vanilla 3D-CNN approaches often divide the 3D space of objects into equal-sized voxels. In contrast, OctSurf recursively partitions the 3D space containing the protein-ligand pocket into eight subspaces called octants. Only those octants containing van der Waals surface points of protein or ligand atoms undergo the recursive subdivision process until they reach the predefined octree depth, whereas unoccupied octants are kept intact to reduce the memory cost. Resulting non-empty leaf octants approximate molecular surfaces of the protein pocket and bound ligands. These surface octants, along with their chemical and geometric features, are used as the input to 3D-CNNs. Two kinds of CNN architectures, VGG and ResNet, are applied to the OctSurf representation to predict binding affinity. The OctSurf representation consumes much less memory than the conventional voxel representation at the same resolution. By restricting the convolution operation to only octants of the smallest size, our method also alleviates the overall computational overhead of CNN. A series of experiments are performed to demonstrate the disk storage and computational efficiency of the proposed learning method. Our code is available at the following GitHub repository: https://github.uconn.edu/mldrugdiscovery/OctSurf.

[Oxygen consumption rate of Sepia pharaonis embryos.] / 虎斑乌贼的胚胎耗氧率.

This research was conducted to unravel the variation of oxygen consumption rate during different developmental stages and the effects of different ecological factors on embryonic oxygen consumption rate of Sepia pharaonis. The oxygen consumption rates were measured at twelve deve-lopmental stages by the sealed volumetric flasks, and four embryonic developmental periods (oosperm, gastrula, the formation of organization, endoskeleton) were selected under various ecological conditions, such as salinity (21, 24, 27, 30, 33), water temperature (18, 21, 24, 27, 30 ℃) and pH (7.0, 7.5, 8.0, 8.5, 9.0). The results showed that the oxygen consumption rate rose along with the developmental progress, and distinctly differed from each other. The oxygen consumption rate was 0.082 mg·(100 eggs)-1·h-1 during oosperm period, and rose to 0.279 mg·(100 eggs)-1·h-1 during gastrula period, which was significantly higher than that of blastula period. Finally, the oxygen consumption rate rose to 1.367 mg·(100 eggs)-1·h-1 during hatching period. The salinity showed a significant effect on oxygen consumption rate during the formation of organization and endoskeleton formation stage (P<0.05), but no significant effect during oosperm and gastrula periods (P>0.05). The oxygen consumption rates of four studied embryonic stages all rose and then declined along with the increase of salinity, and reached the highest values [0.082, 0.200, 0.768 and 1.301 mg·(100 eggs)-1·h-1, respectively] at salinity 30. The water temperature had a significant effect on the embryo oxygen consumption rates of gastrula, and the formation of organization and endoskeleton formation stage (P<0.05), with the exception of oosperm (P>0.05). The oxygen consumption rates of four studied embryonic stages all rose and then declined along with the increase of temperature, and reached the highest values at 27 ℃ [0.082, 0.286, 0.806 and 1.338 mg·(100 eggs)-1·h-1, respectively]. The pH had no significant effect on the oxygen consumption rates of four embryonic stages (P>0.05). The oxygen consumption rates of four studied embryonic stages all rose and then declined along with the increase of pH. The oxygen consumption rates of gastrula, the formation of organization, endoskeleton reached the according highest values [0.281, 0.799 and 1.130 mg·(100 eggs)-1·h-1] at pH 8.5, but that during oosperm period occurred at pH 8.0 [0.116 mg·(100 eggs)-1·h-1].