The visualization of biological networks is critically important to aid researchers in understanding complex biological systems and arouses interest in designing efficient layout algorithms to draw ...biological networks according to their topology structures, especially for those networks with potential modules. The algorithms of grid layout series have an advantage in generating compact layouts with overlap-free nodes compared to force-directed; however, extant grid layout algorithms have difficulty in drawing modular networks and often generate layouts of high visual complexity when applied to networks with dense or clustered connectivity structure. To specifically assist the study of modular networks, we propose a grid- and modularity-based layout algorithm (GML) that consists of three stages: network preprocessing, module layout and grid optimization. The algorithm can draw complex biological networks with or without predefined modules based on the grid layout algorithm. It also outperforms other existing grid-based algorithms in the measurement of computation performance, ratio of edge-edge/node-edge crossings, relative edge lengths, and connectivity F-measures. GML helps users to gain insight into the network global characteristics through module layout, as well as to discern network details with grid optimization. GML has been developed as a VisANT plugin (https://hscz.github.io/Biological-Network-Visualization/) and is freely available to the research community.
Thermally conductive polymer composites (TCPCs) are highly desirable for thermal management in electronic devices and modern electrical systems. However, it still remains a great challenge to ...reconciliate the conflict between thermal conductivity and mechanical properties of TCPCs. Herein, we realized the development of multilayer gradient boron nitride nanosheet/aramid nanofiber (BNNS/ANF) films with excellent thermal conductivity and improved tensile strength. The multilayer gradient BNNS/ANF films achieved a superior in-plane thermal conductivity of 19.13 W/(m K) and a high tensile strength of 59.3 MPa, with 23.6% and 61.6% increases compared to the single-layer BNNS/ANF film at the same BNNS content. Finite element analysis was used to clarify the enhanced mechanism of the multilayer gradient structure on thermal conductivity and tensile strength. These desirable properties demonstrate that the multilayer gradient structure is an efficient strategy to address the conflict between thermal conductivity and mechanical properties, and paves the way for the design and preparation of high-performance TCPCs for thermal management applications.
In this paper we propose and analyze the alternating direction implicit (ADI) difference schemes in conjunction with the second order backward differentiation formula (BDF2) method with variable time ...step sizes for solving the two-dimensional parabolic equation. The spatial compact operators are also applied to construct high order ADI scheme. By using the discrete energy method and the positive definiteness of the nonuniform BDF2 approximation, we prove the unconditional H1 semi-norm stability for the variable-step BDF2-ADI scheme and the variable-step compact BDF2-ADI scheme under the constraint rn≤4.8, where rn denotes the adjacent step size ratio. Moreover, the optimal second order and the fourth order convergence rates are derived rigorously under this restriction. To the best of our knowledge, this is the first strict theoretical analysis of the variable-step ADI numerical schemes for the multidimensional parabolic equations. Several numerical examples are included to verify the analysis results. The extension to the nonlinear Allen-Cahn equation is also presented, for which the variable-step BDF2-ADI scheme and the corresponding compact scheme combined with the adaptive time-stepping algorithm improve the efficiency of the long time simulation.
•Shading stress and variety affected photosynthetic characters and yield of rice.•Chl contents in rice increased, while Pn, ETR, PARsat, and Jmax decreased.•IIyou can be selected as a shade-tolerant ...variety in low-light regions.
Low radiation caused by industrial development and environment change has become a limitation in crop production in China. Field experiments were conducted to investigate the effect of shading stress on photosynthetic and chlorophyll fluorescence characters, as well as grain yield and yield components of rice from 2010 to 2012, in Sichuan, China. Rice cv. IIyou 498, Gangyou 188, Dexiang 4103, Gangyou 527, and Chuanxiang 9838 were selected and shaded during grain filling period, which resulted in 53% shading environment (achieved with white cloth above the rice canopy). Shading increased the flag leaf chlorophyll (Chl) content and maximum efficiency of PSII photochemistry under dark-adaption (Fv/Fm), but decreased the net photosynthetic rate, electron transport rate (ETR), saturation irradiance (PARsat), and maximum electron transport (Jmax), which resulted in a sharply falling grain yield mainly due to reduced spikelet filling and grain weight. The shading tolerances were different in different rice varieties. Maximum net photosynthetic rate (Pmax), light saturation point (LSP), quantum yield of PSII (ΦPSII), and photochemical quenching (qP) of Gangyou 188 were reduced under shading. However, IIyou 498 had its adaptive capacity to shading enhanced by increasing the Chl content to improve light-harvesting potential as well as increased Pmax, LSP, Fv/Fm, and ΦPSII. In addition, there was reduced non-photochemical quenching (NPQ), while maintaining a more stable ETR, PARsat, and Jmax to enhance light-use efficiency and reduce the dissipation of light energy, which relieved damage to spikelet filling and resulted in a smaller reduction in grain yield of IIyou 498. Therefore, the improvement in light-harvesting and -use capability and increased spikelet filling under shading stress might be important characteristics for plant breeders. For example, IIyou 498 can be selected as a shade-tolerant variety.
The mitochondrial and endoplasmic reticulum (ER) homeostasis is pivotal to the maintenance of an array of physiological processes. The physical contact and association between ER and mitochondria, ...known as the ER-mitochondria microdomains or mitochondria-associated ER membrane (MAM), temporally and spatially regulates the mitochondria/ER structure and function. More evidence suggests a role for MAMs in energy production, cellular contraction and mobility, and normal extracellular signal transmission. In pathological states, such as cardiac ischemia-reperfusion (I/R injury), this ER-mitochondria microdomains may act to participate in the cellular redox imbalance, ER stress, mitochondrial injury, energy deletion, and programmed cell death. From a therapeutic perspective, a better understanding of the cellular and molecular mechanisms of the pathogenic ER-mitochondria contact should help to identify potential therapeutic target for cardiac I/R injury and other cardiovascular diseases and also pave the road to new treatment modalities pertinent for the treatment of reperfusion damage in clinical practice. This review will mainly focus on the possible signaling pathways involved in the regulation of the ER-mitochondria contact. In particular, we will summarize the downstream signaling modalities influenced by ER-mitochondria microdomains, for example, mitochondrial fission, mitophagy, calcium balance, oxidative stress, and programmed cell death in details.
Evidence shows that herbal medicine could be beneficial for the treatment of various diseases.The complexity of chemical components of herbal medicine hinders the development of new herbal drugs, ...involving bioactive compounds, action mechanism, and uncertain therapeutic targets.Metabolomics has become an important means for future improvement and understanding of herbal medicine from a small-molecule metabolism level.The chinmedomics-based metabolomics strategy shows great potential for understanding metabolic pathways, evaluating curative effects, clarifying mechanisms, and discovering active ingredients.
Evidence shows that herbal medicine (HM) could be beneficial for the treatment of various diseases. However, complexities present in HM due to the unclear bioactive compounds, mechanisms of action, undetermined targets for therapy, and nonspecific features for metabolism, are currently an obstacle for the progression of novel drug discovery. Metabolomics could be a potential tool to overcome these issues and for the understanding of HM from a small-molecule metabolism level. The chinmedomics-based metabolomics method assesses the overall metabolism of organisms with a holistic view and shows great potential for understanding metabolic pathways, evaluating curative effects, clarifying mechanisms, discovering active ingredients, and precision medicine. This review focuses on the efficacy evaluation, active ingredient discovery, and target exploration of HM based on metabolomics and chinmedomics.
Alcohol abuse is a serious medical and social problem. Although light to moderate alcohol consumption is beneficial to cardiovascular health, heavy drinking often results in organ damage and social ...problems. In addition, genetic susceptibility to the effect of alcohol on cancer and coronary heart disease differs across the population. A number of mechanisms including direct the toxicity of ethanol, its metabolites e.g., acetaldehyde and fatty acid ethyl esters (FAEEs) and oxidative stress may mediate alcoholic complications. Acetaldehyde, the primary metabolic product of ethanol, is an important candidate toxin in developing alcoholic diseases. Meanwhile, free radicals produced during ethanol metabolism and FAEEs are also important triggers for alcoholic damages.
Erianin is a small‐molecule compound that is isolated from Dendrobium chrysotoxum Lindl. In recent years, it has been found to have evident antitumor activity in various cancers, such as bladder ...cancer, cervical cancer, and nasopharyngeal carcinoma. In this study, we assessed the effect of erianin on lung cancer in terms of cell growth inhibition and the related mechanism. First, erianin at a concentration of less than 1 nmol/L exhibited cytotoxicity in H1975, A549, LLC lung cancer cells, did not cause marked growth inhibition in normal lung and kidney cells, induced obvious apoptosis and G2/M phase arrest of cells, and inhibited the migration and invasion of lung cancer cells in vitro. Second, in a mouse xenograft model of lewis lung cancer (LLC), oral administration of erianin (50, 35, and 10 mg kg−1 day−1 for 12 days) substantially inhibited nodule growth, reduced the fluorescence counts of lewis cells and the percentage vascularity of tumor tissues, increased the number of apoptotic tumor cells, the thymus indices, up‐regulated the levels of interleukin (IL)‐2 and tumor necrosis factor‐α (TNF‐α), decreased IL‐10 levels and the spleen index, and enhanced immune function. Lastly, the possible targets of erianin were determined by molecular docking and verified via western blot assay. The results indicated that erianin may achieve the above effects via inhibiting the phosphoinositide 3‐kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway in vitro and vivo. Taken together, the results showed that erianin had obvious antitumor effects via inhibiting the PI3K/Akt/mTOR pathway in vitro and vivo and may have potential clinical value for the treatment of lung cancer.
•Heavy metal concentrations in household dust collected from 6 urban districts.•Health risks were evaluated for the metals combined with oral bioaccessibility.•There was negative correlation between ...the metals concentrations and floor levels.
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To investigate the characteristics of heavy metals (Cr, Cd, Pb, Zn, Cu and Ni) in household dust in urban household environment of Chengdu, China, 90 household dust samples were collected from 6 districts of the city. The information of houses and residents were also recorded during dust sampling to identify the correlations between heavy metals in household dust and the house attributes. And also the principal component analysis and cluster analysis for sources and impactor factors. The concentrations of Pb (123mg·kg−1), Zn (675mg·kg−1), Cu (190mg·kg−1), Cr (82.7mg·kg−1), Cd (2.37mg·kg−1) and Ni (52.6mg·kg−1) in household dust are in low or moderate levels when compare with that from other counties or areas. The heavy metals of household dust samples from Chengdu is higher concentrations than that in the street dust from Chengdu, except for Cr. Statistical analysis result showed traffic sources and corrosion of alloys are important factors contributing to the rise concentrations of heavy metals in household dust. In addition, there is negative correlation (p<0.05) between the heavy metals concentrations and floor levels. The ingestion is the important pathway for Pb, Zn, Cu and Ni via household dust exposure to the residents, and the dermal contact was identified as a main route for Cr and Cd in household dust exposure to the residents. There are minor non-carcinogenic and carcinogenic risks from the heavy metals in household dust for the residents in Chengdu.
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