DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of DNA sequences.

Identifying the function of DNA sequences accurately is an essential and challenging task in the genomic field. Until now, deep learning has been widely used in the functional analysis of DNA sequences, including DeepSEA, DanQ, DeepATT and TBiNet. However, these methods have the problems of high computational complexity and not fully considering the distant interactions among chromatin features, thus affecting the prediction accuracy. In this work, we propose a hybrid deep neural network model, called DeepFormer, based on convolutional neural network (CNN) and flow-attention mechanism for DNA sequence function prediction. In DeepFormer, the CNN is used to capture the local features of DNA sequences as well as important motifs. Based on the conservation law of flow network, the flow-attention mechanism can capture more distal interactions among sequence features with linear time complexity. We compare DeepFormer with the above four kinds of classical methods using the commonly used dataset of 919 chromatin features of nearly 4.9 million noncoding DNA sequences. Experimental results show that DeepFormer significantly outperforms four kinds of methods, with an average recall rate at least 7.058% higher than other methods. Furthermore, we confirmed the effectiveness of DeepFormer in capturing functional variation using Alzheimer's disease, pathogenic mutations in alpha-thalassemia and modification in CCCTC-binding factor (CTCF) activity. We further predicted the maize chromatin accessibility of five tissues and validated the generalization of DeepFormer. The average recall rate of DeepFormer exceeds the classical methods by at least 1.54%, demonstrating strong robustness.

Exercise training decreases lactylation and prevents myocardial ischemia-reperfusion injury by inhibiting YTHDF2.

Exercise improves cardiac function and metabolism. Although long-term exercise leads to circulating and micro-environmental metabolic changes, the effect of exercise on protein post-translational lactylation modifications as well as its functional relevance is unclear. Here, we report that lactate can regulate cardiomyocyte changes by improving protein lactylation levels and elevating intracellular N6-methyladenosine RNA-binding protein YTHDF2. The intrinsic disorder region of YTHDF2 but not the RNA m6A-binding activity is indispensable for its regulatory function in influencing cardiomyocyte cell size changes and oxygen glucose deprivation/re-oxygenation (OGD/R)-stimulated apoptosis via upregulating Ras GTPase-activating protein-binding protein 1 (G3BP1). Downregulation of YTHDF2 is required for exercise-induced physiological cardiac hypertrophy. Moreover, myocardial YTHDF2 inhibition alleviated ischemia/reperfusion-induced acute injury and pathological remodeling. Our results here link lactate and lactylation modifications with RNA m6A reader YTHDF2 and highlight the physiological importance of this innovative post-transcriptional intrinsic regulation mechanism of cardiomyocyte responses to exercise. Decreasing lactylation or inhibiting YTHDF2/G3BP1 might represent a promising therapeutic strategy for cardiac diseases.

Fluid-Solid Interfacial Properties and Drag-Reducing Characterization of the Flexible Conical Microstructured Film Inspired by the Streamlined Body Surface of the Pufferfish.

Given the challenges in accurately replicating the surface of the pufferfish, this study employed three-dimensional (3D) printing to create a model based on inverse modeling. The morphology of the pufferfish exhibits a streamlined configuration, characterized by a gradual widening from the anterior oral region to the central ocular area, followed by a progressive narrowing from the midabdominal region toward the caudal extremity. The RNG k-ε turbulence simulation results demonstrate that the streamlined body surface of the pufferfish diminishes differential pressure resistance. This enhancement promotes laminar flow formation, delays fluid separation, minimizes turbulence-induced vortices, and reduces frictional resistance. Moreover, the pufferfish's supple and uneven outer epidermis was simplified into a flexible, nonsmooth planar film to conduct fluid-solid coupling simulations. These revealed that the pufferfish's unique skin can absorb turbulent energy and minimize momentum transfer between the fluid and the solid film, lowering the fluid resistance during swimming. In summary, The high-efficiency swimming capacity of pufferfish stems not only from their streamlined body surface but also significantly from the unique structural characteristics and mechanical properties of their flexible skin. This research provides critical theoretical underpinnings for the design of functional bionic surfaces aimed at drag reduction.

Superhydrophobic Surfaces with Excellent Ice Prevention and Drag Reduction Properties Inspired by Iridaceae Leaf.

The anti-icing and drag-reduction properties of diverse microstructured surfaces have undergone extensive study over the past decade. Nonetheless, tough environments enforce stringent demands on the composite characteristics of superhydrophobic surfaces (SHS). In this study, fresh composite structures were fabricated on a metal substrate by nanosecond laser machining technology, drawing inspiration from the hardy plant Iridaceae. The prepared sample surface mainly consists of a periodic microrhombus array and irregular nanosheets. To comprehensively investigate the effect of its special structure on surface properties, three surfaces with different sizes of rhombic structures were used for comparative analysis, and the results show that the SH-S2 sample is optimal. This can significantly delay the freezing time by an impressive 1404 s at -10 °C while revealing the sample surface anti-icing strategy. In addition, the rheological experiments determined over 300 µm of slip length for the SH-S2 sample, and the drag reduction rate of the surface reaches nearly 40%, which is well aligned with the results of the delayed icing experiments. Finally, the mechanical durability of the SH-S2 surface was investigated through scratch damage, sandpaper abrasion, reparability trials, and icing and melting cycle tests. This research presents a new approach and methodology for the application of SHS on polar ship surfaces.

Circular RNA Translation in Cardiovascular Diseases.

Circular RNAs (circRNAs) are a class of endogenous functional RNA generated by back-splicing. Recently, circRNAs have been found to have certain coding potential. Proteins/peptides translated from circRNAs play essential roles in various diseases. Here, we briefly summarize the basic knowledge and technologies that are usually applied to study circRNA translation. Then, we focus on the research progress of circRNA translation in cardiovascular diseases and discuss the perspective and future direction of translatable circRNA study in cardiovascular diseases.

Extracellular Vesicles and Hypertension.

Hypertension implicates multiple organs and systems, accounting for the majority of cardiovascular diseases and cardiac death worldwide. Extracellular vesicles derived from various types of cells could transfer a variety of substances such as proteins, lipids, and nucleic acids from cells to cells, playing essential roles in both physiological and pathological processes. Extracellular vesicles are demonstrated to be closely associated with the development of essential hypertension by mediating the renin-angiotensin-aldosterone system and crosstalk between multiple vascular cells. Extracellular vesicles also participate in various kinds of pathogenesis of secondary hypertensions including acute kidney injury, renal parenchymal diseases, kidney transplantation, secretory diseases (primary aldosteronism, pheochromocytoma and paraganglioma, Cushing's syndrome), and obstructive sleep apnea. Extracellular vesicles have been proved to have the potential to be served as new biomarkers in the diagnosis, treatment, and prognosis assessment of hypertension. In the future, large multicenter cohorts are highly in demand for further verifying the sensitivity and specificity of extracellular vesicles as biomarkers.

Adsorption removal of cationic dyes from aqueous solutions using ceramic adsorbents prepared from industrial waste coal gangue.

Industrial solid waste coal gangue has huge utilization potential. Low-cost ceramic microsphere adsorbents were prepared from coal gangue by spray drying and sintering method and applied to remove cationic red X-5GN and cationic blue X-GRRL from aqueous solutions. The structural properties of the adsorbents were characterized. Adsorption kinetics, adsorption isotherms and effect of solution pH were studied. Adsorption mechanism and disposal of the spent adsorbents were also discussed. The results showed that the adsorption capacity of the cationic red and cationic blue onto the ceramic adsorbents was 1.044 mg g-1 and 2.170 mg g-1 respectively, according to the Langmuir model. The adsorption equilibrium time was quickly reached with the removal of both dyes over 90% within 1 min. The adsorbents exhibited favorable applicability with varying solution pH. Electrostatic attractions, n-π interactions and hydrogen bonding were proposed to be involved in the adsorption process based on the adsorption behavior. Using coal gangue ceramic adsorbents to treat colored wastewater could achieve the purpose of treating wastes with wastes. Therefore, the gangue adsorbent has promising application prospects for its comprehensive economic and environmental benefits.

Water use efficiency of China's karst ecosystems: The effect of different ecohydrological and climatic factors.

Water use efficiency (WUE) is an important indicator for understanding the coupled ecosystem carbon and water cycles. However, the effect and contributions of factors on WUE variations in China's karst ecosystems for different climatic conditions have not been extensively studied. Our studies on WUE variations of China's karst ecosystems from 2001 to 2021 based on evapotranspiration and net primary productivity (NPP) from Moderate-resolution imaging spectroradiometer revealed the contributions of soil moisture (SM), leaf area index (LAI), precipitation (P), temperature (T), vapor pressure deficit (VPD), and CO2 concentration (CO2). Results showed that the trend of WUE was similar to that of NPP in terms of the latitude, longitude, and elevation, and WUE started abruptly decreasing after an elevation >3000 m until it reached 0 at 4500 m. WUE was primarily "slightly increased" in the humid region (H) and "slightly decreased" in the semi-humid region (SH), arid and semi-arid regions (ASA), and Qinghai-Tibet plateau region (QTP). CO2 (0.34), LAI (0.60), P (0.58), and LAI (0.55) exhibited the strongest positive direct effects on WUE in H, SH, ASA, and QTP, while VPD exhibited the strongest negative direct effect. VPD (0.26), VPD (0.28), SM (0.47), and P (0.39) had the strongest positive indirect effect, while T (-0.24), T (-0.18), VPD (-0.35), and P (-0.03) had the strongest negative indirect effect on WUE. The positive contributions of WUE variations in H, SH, ASA, and QTP were dominated by T (47.96 %), CO2 (26.36 %), P (8.81 %), and CO2 (52.97 %), whereas the negative contributions were dominated by P (-7.95 %), LAI (-26.57 %), CO2 (-35.98 %), and VPD (-9.59 %), respectively. This study quantifies the spatial and temporal distribution patterns of WUE in China's karst ecosystems and the regional differences between the multiple ecohydrological factors, thereby facilitating in-depth understanding and effective regulation for the carbon and water cycles in karst ecosystems.