Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution.

In flowering plants, C4 photosynthesis is superior to C3 type in carbon fixation efficiency and adaptation to extreme environmental conditions, but the mechanisms behind the assembly of C4 machinery remain elusive. This study attempts to dissect the evolutionary divergence from C3 to C4 photosynthesis in five photosynthetic model plants from the grass family, using a combined comparative transcriptomics and deep learning technology. By examining and comparing gene expression levels in bundle sheath and mesophyll cells of five model plants, we identified 16 differentially expressed signature genes showing cell-specific expression patterns in C3 and C4 plants. Among them, two showed distinctively opposite cell-specific expression patterns in C3 vs. C4 plants (named as FOGs). The in silico physicochemical analysis of the two FOGs illustrated that C3 homologous proteins of LHCA6 had low and stable pI values of ~6, while the pI values of LHCA6 homologs increased drastically in C4 plants Setaria viridis (7), Zea mays (8), and Sorghum bicolor (over 9), suggesting this protein may have different functions in C3 and C4 plants. Interestingly, based on pairwise protein sequence/structure similarities between each homologous FOG protein, one FOG PGRL1A showed local inconsistency between sequence similarity and structure similarity. To find more examples of the evolutionary characteristics of FOG proteins, we investigated the protein sequence/structure similarities of other FOGs (transcription factors) and found that FOG proteins have diversified incompatibility between sequence and structure similarities during grass family evolution. This raised an interesting question as to whether the sequence similarity is related to structure similarity during C4 photosynthesis evolution.

Flipover outperforms dropout in deep learning.

Flipover, an enhanced dropout technique, is introduced to improve the robustness of artificial neural networks. In contrast to dropout, which involves randomly removing certain neurons and their connections, flipover randomly selects neurons and reverts their outputs using a negative multiplier during training. This approach offers stronger regularization than conventional dropout, refining model performance by (1) mitigating overfitting, matching or even exceeding the efficacy of dropout; (2) amplifying robustness to noise; and (3) enhancing resilience against adversarial attacks. Extensive experiments across various neural networks affirm the effectiveness of flipover in deep learning.

The time course of planar and non-planar rotations in a letter rotation task.

Mental rotation (MR) of character letters requires participants to mentally rotate the letter in their minds' eyes through a process akin to the physical rotation of the stimulus. It has been suggested that different cognitive processes are engaged during such MR of both canonical and mirror-reversed letters. In addition to the planar rotation of the canonical letters, an additional "flip-over" process (non-planar rotation) has been assumed during the MR of mirror-reversed letters. However, the temporal relationship between planar and non-planar rotation has not been systematically investigated. In this study, the occurrence of both planar and non-planar rotations were examined through the analysis of the event-related brain potentials (ERPs) elicited by canonical or mirror-reversed letters presented at different rotation angles between 300 and 1000 ms post-stimulus onset over consecutive 50ms time-windows. For smaller rotation angles (30° and 60°), non-planar rotation preceded planar rotation. For letters rotated by 90°, planar and non-planar rotation occurred at the same time. For larger angles (120° and 150°), the letter was first rotated within the plane (planar rotation) and afterwards it was also rotated out-of-the-plane (non-planar rotation) until it was fully canonicalized. Thus, the temporal relationship between planar and non-planar rotation differed for each rotation angle, with the non-planar rotation occurring at increasingly later intervals for different points in time for progressively larger rotation angles. These findings have relevant methodological implications for studies investigating the psychophysiological correlates of the mental rotation of mirror letters.