Development of a novel copper metabolism-related risk model to predict prognosis and tumor microenvironment of patients with stomach adenocarcinoma

Background: Stomach adenocarcinoma (STAD) is the fourth highest cause of cancer mortality worldwide. Alterations in copper metabolism are closely linked to cancer genesis and progression. We aim to identify the prognostic value of copper metabolism-related genes (CMRGs) in STAD and the characteristic of the tumor immune microenvironment (TIME) of the CMRG risk model.Methods: CMRGs were investigated in the STAD cohort from The Cancer Genome Atlas (TCGA) database. Then, the hub CMRGs were screened out with LASSO Cox regression, followed by the establishment of a risk model and validated by GSE84437 from the Expression Omnibus (GEO) database. The hub CMRGs were then utilized to create a nomogram. TMB (tumor mutation burden) and immune cell infiltration were investigated. To validate CMRGs in immunotherapy response prediction, immunophenoscore (IPS) and IMvigor210 cohort were employed. Finally, data from single-cell RNA sequencing (scRNA-seq) was utilized to depict the properties of the hub CMRGs.Results: There were 75 differentially expressed CMRGs identified, 6 of which were linked with OS. 5 hub CMRGs were selected by LASSO regression, followed by construction of the CMRG risk model. High-risk patients had a shorter life expectancy than those low-risk. The risk score independently predicted STAD survival through univariate and multivariate Cox regression analyses, with ROC calculation generating the highest results. This risk model was linked to immunocyte infiltration and showed a good prediction performance for STAD patients’ survival. Furthermore, the high-risk group had lower TMB and somatic mutation counters and higher TIDE scores, but the low-risk group had greater IPS-PD-1 and IPS-CTLA4 immunotherapy prediction, indicating a higher immune checkpoint inhibitors (ICIs) response, which was corroborated by the IMvigor210 cohort. Furthermore, those with low and high risk showed differential susceptibility to anticancer drugs. Based on CMRGs, two subclusters were identified. Cluster 2 patients had superior clinical results. Finally, the copper metabolism-related TIME of STAD was concentrated in endothelium, fibroblasts, and macrophages.Conclusion: CMRG is a promising biomarker of prognosis for patients with STAD and can be used as a guide for immunotherapy

MHNF: Multi-hop Heterogeneous Neighborhood information Fusion graph representation learning

Attention mechanism enables the Graph Neural Networks(GNNs) to learn the attention weights between the target node and its one-hop neighbors, the performance is further improved. However, the most existing GNNs are oriented to homogeneous graphs and each layer can only aggregate the information of one-hop neighbors. Stacking multi-layer networks will introduce a lot of noise and easily lead to over smoothing. We propose a Multi-hop Heterogeneous Neighborhood information Fusion graph representation learning method (MHNF). Specifically, we first propose a hybrid metapath autonomous extraction model to efficiently extract multi-hop hybrid neighbors. Then, we propose a hop-level heterogeneous Information aggregation model, which selectively aggregates different-hop neighborhood information within the same hybrid metapath. Finally, a hierarchical semantic attention fusion model (HSAF) is proposed, which can efficiently integrate different-hop and different-path neighborhood information respectively. This paper can solve the problem of aggregating the multi-hop neighborhood information and can learn hybrid metapaths for target task, reducing the limitation of manually specifying metapaths. In addition, HSAF can extract the internal node information of the metapaths and better integrate the semantic information of different levels. Experimental results on real datasets show that MHNF is superior to state-of-the-art methods in node classification and clustering tasks (10.94% - 69.09% and 11.58% - 394.93% relative improvement on average, respectively)

Structure of the substrate-engaged SecA-SecY protein translocation machine.

The Sec61/SecY channel allows the translocation of many proteins across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. In bacteria, most secretory proteins are transported post-translationally through the SecY channel by the SecA ATPase. How a polypeptide is moved through the SecA-SecY complex is poorly understood, as structural information is lacking. Here, we report an electron cryo-microscopy (cryo-EM) structure of a translocating SecA-SecY complex in a lipid environment. The translocating polypeptide chain can be traced through both SecA and SecY. In the captured transition state of ATP hydrolysis, SecAs two-helix finger is close to the polypeptide, while SecAs clamp interacts with the polypeptide in a sequence-independent manner by inducing a short β-strand. Taking into account previous biochemical and biophysical data, our structure is consistent with a model in which the two-helix finger and clamp cooperate during the ATPase cycle to move a polypeptide through the channel

Interfacial Interaction Enhanced Rheological Behavior in PAM/CTAC/Salt Aqueous Solution—A Coarse-Grained Molecular Dynamics Study

Interfacial interactions within a multi-phase polymer solution play critical roles in processing control and mass transportation in chemical engineering. However, the understandings of these roles remain unexplored due to the complexity of the system. In this study, we used an efficient analytical method—a nonequilibrium molecular dynamics (NEMD) simulation—to unveil the molecular interactions and rheology of a multiphase solution containing cetyltrimethyl ammonium chloride (CTAC), polyacrylamide (PAM), and sodium salicylate (NaSal). The associated macroscopic rheological characteristics and shear viscosity of the polymer/surfactant solution were investigated, where the computational results agreed well with the experimental data. The relation between the characteristic time and shear rate was consistent with the power law. By simulating the shear viscosity of the polymer/surfactant solution, we found that the phase transition of micelles within the mixture led to a non-monotonic increase in the viscosity of the mixed solution with the increase in concentration of CTAC or PAM. We expect this optimized molecular dynamic approach to advance the current understanding on chemical–physical interactions within polymer/surfactant mixtures at the molecular level and enable emerging engineering solutions

Self-optimizing Feature Generation via Categorical Hashing Representation and Hierarchical Reinforcement Crossing

Feature generation aims to generate new and meaningful features to create a discriminative representation space.A generated feature is meaningful when the generated feature is from a feature pair with inherent feature interaction. In the real world, experienced data scientists can identify potentially useful feature-feature interactions, and generate meaningful dimensions from an exponentially large search space, in an optimal crossing form over an optimal generation path. But, machines have limited human-like abilities.We generalize such learning tasks as self-optimizing feature generation. Self-optimizing feature generation imposes several under-addressed challenges on existing systems: meaningful, robust, and efficient generation. To tackle these challenges, we propose a principled and generic representation-crossing framework to solve self-optimizing feature generation.To achieve hashing representation, we propose a three-step approach: feature discretization, feature hashing, and descriptive summarization. To achieve reinforcement crossing, we develop a hierarchical reinforcement feature crossing approach.We present extensive experimental results to demonstrate the effectiveness and efficiency of the proposed method. The code is available at https://github.com/yingwangyang/HRC_feature_cross.git

Cam Drive Step Mechanism of a Quadruped Robot

Bionic quadruped robots received considerable worldwide research attention. For a quadruped robot walking with steady paces on a flat terrain, using a cam drive control mechanism instead of servomotors provides theoretical and practical benefits as it reduces the system weight, cost, and control complexities; thus it may be more cost beneficial for some recreational or household applications. This study explores the robot step mechanism including the leg and cam drive control systems based on studying the bone structure and the kinematic step sequences of dog. The design requirements for the cam drive robot legs have been raised, and the mechanical principles of the leg operating mechanism as well as the control parameters have been analyzed. A cam drive control system was constructed using three cams to control each leg. Finally, a four-leg demo robot was manufactured for experiments and it showed stable walking patterns on a flat floor

Simultaneous separation and purification of chlorogenic acid, epicatechin, hyperoside and phlorizin from thinned young Qinguan apples by successive use of polyethylene and polyamide resins

The method for separating and purifying chlorogenic acid (CA), epicatechin (EC), hyperoside (HY) and phlorizin (PH) simutaneously from young Qinguan apples by successive use of X-5 and polyamide resins has been developed in this study. The order of adsorption capacities of X-5 for the four phenolics was PH\ua0>\ua0HY\ua0>\ua0EC\ua0>\ua0CA, and the adsorption equilibriums of the four phenolics onto X-5 resin conformed to Langmuir isotherms preferentially. The adsorption kinetics of EC and CA onto X-5 conformed to the pseudo-first-order model, while that of HY and PH accorded with the pseudo-second-order model. Interestingly, the values of equilibrium adsorption capacities (Q) calculated in the preferential kinetics models were closer to that of theoretical maximum adsorption capacities (Q) calculated by Langmuir isotherms. Through dynamic adsorption and desorption using X-5 and polyamide resins with ethanol solution as strippant, CA, EC, HY and PH were obtained with purities of 96.21%, 95.34%, 95.36% and 97.36%, respectively

Reactive oxygen species may be involved in the distinctive biological effects of different doses of 12C6+ ion beams on Arabidopsis

IntroductionHeavy ion beam is a novel approach for crop mutagenesis with the advantage of high energy transfer line density and low repair effect after injury, however, little investigation on the biological effect on plant was performed. 50 Gy irradiation significantly stimulated the growth of Arabidopsis seedlings, as indicated by an increase in root and biomass, while 200 Gy irradiation significantly inhibited the growth of seedlings, causing a visible decrease in plant growth.MethodsThe Arabidopsis seeds were irradiated by 12C6+. Monte Carlo simulations were used to calculate the damage to seeds and particle trajectories by ion implantation. The seed epidermis received SEM detection and changes in its organic composition were detected using FTIR. Evidence of ROS and antioxidant systems were analyzed. RNA-seq and qPCR were used to detect changes in seedling transcript levels.Results and discussionMonte Carlo simulations revealed that high-dose irradiation causes various damage. Evidence of ROS and antioxidant systems implies that the emergence of phenotypes in plant cells may be associated with oxidative stress. Transcriptomic analysis of the seedlings demonstrated that 170 DEGs were present in the 50 Gy and 200 Gy groups and GO enrichment indicated that they were mainly associated with stress resistance and cell wall homeostasis. Further GO enrichment of DEGs unique to 50 Gy and 200 Gy revealed 58 50Gy-exclusive DEGs were enriched in response to oxidative stress and jasmonic acid entries, while 435 200 Gy-exclusive DEGs were enriched in relation to oxidative stress, organic cyclic compounds, and salicylic acid. This investigation advances our insight into the biological effects of heavy ion irradiation and the underlying mechanisms