Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding.

MOTIVATION: Gene regulatory networks (GRNs) encode gene regulation in living organisms, and have become a critical tool to understand complex biological processes. However, due to the dynamic and complex nature of gene regulation, inferring GRNs from scRNA-seq data is still a challenging task. Existing computational methods usually focus on the close connections between genes, and ignore the global structure and distal regulatory relationships. RESULTS: In this study, we develop a supervised deep learning framework, IGEGRNS, to infer GRNs from scRNA-seq data based on graph embedding. In the framework, contextual information of genes is captured by GraphSAGE, which aggregates gene features and neighborhood structures to generate low-dimensional embedding for genes. Then, the k most influential nodes in the whole graph are filtered through Top-k pooling. Finally, potential regulatory relationships between genes are predicted by stacking CNNs. Compared with nine competing supervised and unsupervised methods, our method achieves better performance on six time-series scRNA-seq datasets. AVAILABILITY AND IMPLEMENTATION: Our method IGEGRNS is implemented in Python using the Pytorch machine learning library, and it is freely available at https://github.com/DHUDBlab/IGEGRNS.

Dissolution-Induced Surface Reconstruction of Ni0.95 Pt0.05 Si/p-Si Photocathode for Efficient Photoelectrochemical H2 Production.

Metal silicide/Si photoelectrodes have demonstrated significant potential for application in photoelectrochemical (PEC) water splitting to produce H2 . To achieve an efficient and economical hydrogen evolution reaction (HER), a paramount consideration lies in attaining exceptional catalytic activity on the metal silicide surface with minimal use of noble metals. Here, this study presents the design and construction of a novel Ni0.95 Pt0.05 Si/p-Si photocathode. Dopant segregation is used to achieve a Schottky barrier height as high as 1.0 eV and a high photovoltage of 420 mV. To achieve superior electrocatalytic activity for HER, a dissolution-induced surface reconstruction (SR) strategy is proposed to in situ convert surface Ni0.95 Pt0.05 Si to highly active Pt2 Si. The resulting SR Ni0.95 Pt0.05 Si/p-Si photocathode exhibits excellent HER performance with an onset potential of 0.45 V (vs RHE) and a high maximum photocurrent density of 40.5 mA cm-2 and a remarkable applied bias photon-to-current efficiency (ABPE) of 5.3% under simulated AM 1.5 (100 mW cm-2 ) illumination. The anti-corrosion silicide layer effectively protects Si, ensuring excellent stability of the SR Ni0.95 Pt0.05 Si/p-Si photoelectrode. This study highlights the potential for achieving efficient PEC HER using bimetallic silicide/Si photocathodes with reduced Pt consumption, offering an auspicious perspective for the cost-effective conversion of solar energy to chemical energy.

Constructing Dynamic Anode/Electrolyte Interfaces Coupled with Regulated Solvation Structures for Long-Term and Highly Reversible Zinc Metal Anodes.

Aqueous zinc ion batteries (AZIBs) show a great potential for next-generation energy storage due to their high safety and high energy density. However, the severe side reactions of zinc negative electrode largely hinder the further application of AZIBs. Herein, trace tris(hydroxymethyl)aminomethane (Tris) additive with rich lone-pair-electrons and zincophilic sites is firstly introduced to achieve long-term and highly reversible Zn plating/stripping. Specifically, Tris not only regulates the solvation structure of Zn2+, but is also adsorbed vertically on the Zn anode surface with a changed coordination intensity during the plating/stripping process of Zn to generate an in situ dynamic adsorption layer for the first time. The dynamic adsorption layer could successively attract the solvated Zn2+ and then promote the de-solvation of the solvated Zn2+ owing to the orientation polarization with regularly-changed applied electric field, the volume rejection effect, and strong intermolecular force towards H2O of the vertically-adsorbed Tris. Therefore, an improved Zn2+-transport kinetics as well as the inhibition of side reactions of Zn anode are successfully realized. Accordingly, the Zn||Zn symmetric cell provides an ultra-long cycle life of 2600 h. Furthermore, the Zn||MnO2 full cell with Tris could demonstrate a high capacity and structural stability for practical applications.

Complex Topology of Ubiquitin Chains Mediates Lysosomal Degradation of MrgC Proteins.

BACKGROUND: Activation of Mas-related G protein-coupled receptor C (MrgC) receptors relieves pain, but also leads to ubiquitination of MrgC receptors. Ubiquitination mediates MrgC receptor endocytosis and degradation. However, MrgC degradation pathways and ubiquitin-linked chain types are not known. METHODS: N2a cells were treated with cycloheximide (CHX, protein synthesis inhibitor), Mg132 (proteasome inhibitor), 3-Methyladenine (3MA, autophagy lysosome inhibitor) and Chloroquine (CQ, autophagy lysosome inhibitor) to observe the half-life and degradation pathway of MrgC. The location of internalized MrgC receptors and lysosomes (Lyso-Tracker) was observed by immunofluorescence staining. N2a cells were transfected with Myc-MrgC and a series of HA-tagged ubiquitin mutants to study the ubiquitin-linked chain type of MrgC. RESULTS: The amount of MrgC protein decreased with time after CHX treatment of N2a cells. Autophagy lysosome inhibitors can inhibit the degradation of MrgC. The amount of MrgC protein decreased with time after CHX treatment of N2a cells. 3-MA and CQ inhibited the degradation of MrgC protein, whereas Mg-132 did not inhibit it. Partially internalized MrgC receptors were co-labeled with lysosomes. MrgC proteins have multiple topologies of ubiquitin-modified chains. CONCLUSION: As a member of the G protein-coupled receptor family, MrgC receptors can be degraded over time. The complex topology of the ubiquitin-linked chain mediates the lysosomal degradation of MrgC proteins.

Photoelectrocatalytic Utilization of CO2 : A Big Show of Si-based Photoelectrodes.

CO2 is a greenhouse gas that contributes to environmental deterioration; however, it can also be utilized as an abundant C1 resource for the production of valuable chemicals. Solar-driven photoelectrocatalytic (PEC) CO2 utilization represents an advanced technology for the resourcing of CO2 . The key to achieving PEC CO2 utilization lies in high-performance semiconductor photoelectrodes. Si-based photoelectrodes have attracted increasing attention in the field of PEC CO2 utilization due to their suitable band gap (1.1 eV), high carrier mobility, low cost, and abundance on Earth. There are two pathways to PEC CO2 utilization using Si-based photoelectrodes: direct reduction of CO2 into small molecule fuels and chemicals, and fixation of CO2 with organic substrates to generate high-value chemicals. The efficiency and product selectivity of PEC CO2 utilization depends on the structures of the photoelectrodes as well as the composition, morphology, and size of the catalysts. In recent years, significant and influential progress has been made in utilizing Si-based photoelectrodes for PEC CO2 utilization. This review summarizes the latest research achievements in Si-based PEC CO2 utilization, with a particular emphasis on the mechanistic understanding of CO2 reduction and fixation, which will inspire future developments in this field.

A multi-center, single-blinded, randomized, parallel-group, superiority study to compare the efficacy of manipulation under anesthesia versus intra-articular steroid injection in the treatment of patients with frozen shoulder and a diagnosis of rotator cuff injury or tear by MRI: study protocol for a randomized controlled trial.

BACKGROUND: Frozen shoulder (FS) is a common condition that can cause severe pain and limited range of motion in the shoulder joint. While intra-articular steroid injection has been shown to be an effective treatment for FS, manipulation under anesthesia (MUA) is an alternative treatment that has gained popularity in recent years. However, there is a lack of evidence regarding the effectiveness of MUA on FS patients with concomitant rotator cuff injury or tear. Though a few studies have shown that MUA is not associated with rotator cuff tears, and will not exacerbate the injury, more high-quality studies with bigger sample sizes are needed. Therefore, the aim of this multi-center, single-blinded, randomized, parallel-group, superiority study is to compare the efficacy of MUA versus intra-articular steroid injection in the treatment of FS patients with a diagnosis of rotator cuff injury or tear by MRI. METHODS: A parallel, single-blinded, multi-center randomized controlled trial of 320 patients will be conducted at three hospitals of China. Eligible patients with frozen shoulder and rotator cuff injury or tear diagnosed by MRI will be randomly assigned to, in equal proportions, the manipulation under anesthesia group and the intra-articular steroid injection group via a central randomization system, undergoing a corresponding operation on day one and a sequent physical exercise for 14 days. The primary outcome is the comprehensive efficacy evaluation (total effective rate) and the change of Constant-Murley Score. Outcome assessors and data analysts will be blinded, and participants will be asked not to reveal their allocation to assessors. DISCUSSION: This study aims to explore the superiority of manipulation under anesthesia in reducing pain and improving shoulder function in frozen shoulder patients accompanied with rotator cuff injury. To provide a scientific basis for the dissemination and application of manipulation under anesthesia, and a better knowledge for the role of MUA in the treatment of frozen shoulder accompanied with rotator cuff injury. TRIAL REGISTRATION: Chictr.org.cn ChiCTR2200067122 . Registered on 27 December 2022. ChiCTR is a primary registry of the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) network and includes all items from the WHO Trial Registration data set in Trial registration.

Heterologous expression of a deacetylase and its application in L-glufosinate preparation.

With potent herbicidal activity, biocatalysis synthesis of L-glufosinate has drawn attention. In present research, NAP-Das2.3, a deacetylase capable of stereoselectively resolving N-acetyl-L-glufosinate to L-glufosinate mined from Arenimonas malthae, was heterologously expressed and characterized. In Escherichia coli, NAP-Das2.3 activity only reached 0.25 U/L due to the formation of inclusive bodies. Efficient soluble expression of NAP-Das2.3 was achieved in Pichia pastoris. In shake flask and 5 L bioreactor fermentation, NAP-Das2.3 activity by recombinant P. pastoris reached 107.39 U/L and 1287.52 U/L, respectively. The optimum temperature and pH for N-acetyl-glufosinate hydrolysis by NAP-Das2.3 were 45 °C and pH 8.0, respectively. The Km and Vmax of NAP-Das2.3 towards N-acetyl-glufosinate were 25.32 mM and 19.23 µmol mg-1 min-1, respectively. Within 90 min, 92.71% of L-enantiomer in 100 mM racemic N-acetyl-glufosinate was converted by NAP-Das2.3. L-glufosinate with high optical purity (e.e.P above 99.9%) was obtained. Therefore, the recombinant NAP-Das2.3 might be an alternative for L-glufosinate biosynthesis.

Amorphous Ni-Mo-B-O Bifunctional Electrocatalyst for Simultaneous Production of Hydrogen and Value-added Chemicals.

Hydrogen evolution reaction (HER) coupled with biomass conversion is a sustainable route to produce clean energy H2 and value-added chemicals simultaneously. Herein, an amorphous Ni-Mo-B-O bifunctional electrocatalyst was synthesized through a facile electrodeposition method and employed as a cathode for HER to produce H2 and as an anode for the conversion of hydroxymethylfurfural (HMF) to furandicarboxylic acid (FDCA). Besides leading to the formation of amorphous structures, the introduction of Mo and B can increase the electron density and optimize the electronic structure of the electrocatalyst, thus substantially increasing the catalytic activity of the catalyst. After continuous reaction at a constant potential of 0.58 V vs. Hg/HgO for 8 hours, the conversion of HMF reached 98.86 %, and the selectivity of the target product FDCA was as high as 92.97 %. Finally, a two-electrolyzer system was constructed using the amorphous Ni-Mo-B-O as both cathode and anode to achieve simultaneous H2 production in the cathode chamber and FDCA production in the anode chamber at a low voltage. This work presents a promising strategy for the design and synthesis of high-performance non-noble metal electrocatalysts for efficient and cost-effective H2 production.

A solar-driven degradation-evaporation strategy for membrane self-cleaning in the efficient separation of viscous crude oil/water emulsions.

Membrane separation techniques are promising methods for effectively treating hazardous emulsified oily wastewater, but membrane fouling remains a serious challenge because the high viscosity and complex composition of crude oil make it easy to adhere to membranes and difficult to be removed by conventional physical or chemical cleaning means. Herein, a two-stage solar-driven (photo-Fenton degradation/evaporation) strategy was proposed to realize the self-cleaning of membranes fouled by viscous crude oil (>60,000 mPa s), wherein the photo-Fenton process helped to degrade the heavy components into light components, and all light components removed during the solar-driven evaporation process. A 1D/2D heterostructure membrane with photo-Fenton activity and anti-crude-oil-fouling performance was prepared via a facile self-assembly vacuum-assist method. The addition of rod-like g-C3N4 (RCN) increased the interlayer distance of α-FeOOH/porous g-C3N4 (FPCN) nanosheets, resulting in a high permeation flux. The FPCN-RCN membrane exhibited both high permeation flux of 779 ± 19 L m-2h-1bar-1 and a separation efficiency of 99.4% for highly viscous crude oil-in-water emulsion. Importantly, the viscous crude oil fouled on the membrane was completely removed by the photo-Fenton degradation/solar-driven evaporation strategy, and the flux recovery rate of the membrane was ∼100%. Therefore, the FPCN-RCN membrane combined with the novel self-cleaning strategy exhibits great potential for practical emulsified oily wastewater treatment.

Artificial intelligence for waste management in smart cities: a review.

The rising amount of waste generated worldwide is inducing issues of pollution, waste management, and recycling, calling for new strategies to improve the waste ecosystem, such as the use of artificial intelligence. Here, we review the application of artificial intelligence in waste-to-energy, smart bins, waste-sorting robots, waste generation models, waste monitoring and tracking, plastic pyrolysis, distinguishing fossil and modern materials, logistics, disposal, illegal dumping, resource recovery, smart cities, process efficiency, cost savings, and improving public health. Using artificial intelligence in waste logistics can reduce transportation distance by up to 36.8%, cost savings by up to 13.35%, and time savings by up to 28.22%. Artificial intelligence allows for identifying and sorting waste with an accuracy ranging from 72.8 to 99.95%. Artificial intelligence combined with chemical analysis improves waste pyrolysis, carbon emission estimation, and energy conversion. We also explain how efficiency can be increased and costs can be reduced by artificial intelligence in waste management systems for smart cities.

USP48 alleviates bone cancer pain and regulates MrgC stabilization in spinal cord neurons of male mice.

BACKGROUND: Ubiquitin-mediated degradation of the Mas-related G protein-coupled receptor C (MrgC) reduces the number of receptors. However, the specific deubiquitinating enzyme antagonize this process has not been reported. In this study, we investigated the effect of ubiquitin-specific protease-48 (USP48) on bone cancer pain (BCP) and its effect on MrgC. METHODS: A mouse model of BCP was established. BCP behaviours of mice were assessed after intrathecal injection of adeno-associated virus (AAV)-USP48. USP48 and MrgC interactions were studied by immunoprecipitation. Overexpression and knockdown of USP48 were conducted in N2a cells to investigate the effect of USP48 on MrgC receptor number and ubiquitination. RESULTS: Spinal cord level USP48 expression was reduced in mice with BCP. Intrathecal injection of AAV-USP48 increased paw withdrawal mechanical threshold and reduced spontaneous flinching in mice. In N2a cells, there were increased number of MrgC receptors after overexpression of USP48 and decreased number of MrgC receptors after knockdown of USP48. USP48 interacted with MrgC and overexpression of USP48 altered the level of ubiquitination of MrgC. CONCLUSION: USP48 antagonizes ubiquitin-mediated autophagic degradation of MrgC and alleviates BCP in a murine animal model. Our findings may provide a new perspective for the treatment of BCP. SIGNIFICANCE: Our finding may provide an important theoretical basis as well as an intervention target for clinical development of drugs for BCP.

A Framework for Multiclass Contour Visualization.

Multiclass contour visualization is often used to interpret complex data attributes in such fields as weather forecasting, computational fluid dynamics, and artificial intelligence. However, effective and accurate representations of underlying data patterns and correlations can be challenging in multiclass contour visualization, primarily due to the inevitable visual cluttering and occlusions when the number of classes is significant. To address this issue, visualization design must carefully choose design parameters to make visualization more comprehensible. With this goal in mind, we proposed a framework for multiclass contour visualization. The framework has two components: a set of four visualization design parameters, which are developed based on an extensive review of literature on contour visualization, and a declarative domain-specific language (DSL) for creating multiclass contour rendering, which enables a fast exploration of those design parameters. A task-oriented user study was conducted to assess how those design parameters affect users' interpretations of real-world data. The study results offered some suggestions on the value choices of design parameters in multiclass contour visualization.

Enhanced Magnetic Hyperthermia of Magnetoferritin through Synthesis at Elevated Temperature.

Iron oxide nanoparticles have attracted a great deal of research interest in recent years for magnetic hyperthermia therapy owing to their biocompatibility and superior thermal conversion efficiency. Magnetoferritin is a type of biomimetic superparamagnetic iron oxide nanoparticle in a ferritin cage with good monodispersity, biocompatibility, and natural hydrophilicity. However, the magnetic hyperthermic efficiency of this kind of nanoparticle is limited by the small size of the mineral core as well as its low synthesis temperature. Here, we synthesized a novel magnetoferritin particle by using a recombinant ferritin from the hyperthermophilic archaeon Pyrococcus furiosus as a template with high iron atom loading of 9517 under a designated temperature of 90 °C. Compared with the magnetoferritins synthesized at 45 and 65 °C, the one synthesized at 90 °C displays a larger average magnetite and/or maghemite core size of 10.3 nm. This yields an increased saturation magnetization of up to 49.6 emu g-1 and an enhanced specific absorption rate (SAR) of 805.3 W g-1 in an alternating magnetic field of 485.7 kHz and 49 kA m-1. The maximum intrinsic loss power (ILP) value is 1.36 nHm2 kg-1. These results provide new insights into the biomimetic synthesis of magnetoferritins with enhanced hyperthermic efficiency and demonstrate the potential application of magnetoferritin in the magnetic hyperthermia of tumors.

MicroRNA-based regulatory mechanisms underlying the synergistic antioxidant action of quercetin and catechin in H2O2-stimulated HepG2 cells: Roles of BACH1 in Nrf2-dependent pathways.

The microRNA-based mechanisms underlying the antioxidant action(s) of co-existing flavonoids in response to oxidative stress are of high interest. This study aimed to extend the existing knowledge and provide insights into the potential regulatory network in response to oxidative stress and the co-presence of quercetin and catechin antioxidants, via a preclinical approach using H2O2-stimulated HepG2 cells. It was confirmed that BACH1 serves as an essential and direct negative regulator of the Keap1-Nrf2 signaling pathway and the antioxidant synergism between quercetin and catechin. BACH1 promoted reactive oxygen species (ROS) accumulation while inhibiting cell growth, which could be reversed by the synergistic action of let-7a-5p and miR-25-3p in the co-presence of quercetin and catechin. Both let-7a-5p and miR-25-3p could directly regulate the expression and function of BACH1 (e.g. upregulation of the two miRNAs could rescue largely overexpression of BACH1). Although these molecular interactions likely represented only some aspects of the overall regulatory network, this research confirms the feasibility of the combined uses of dietary flavonoids with chemopreventive properties in synergy during multiple-target interactions and multiple-pathway regulation.

Clemastine Fumarate Protects Against Myocardial Ischemia Reperfusion Injury by Activating the TLR4/PI3K/Akt Signaling Pathway.

Our pilot studies have shown that clemastine fumarate (CLE) can protect against myocardial ischemia-reperfusion injury (MIRI) through regulation of toll like receptor 4 (TLR4). However, the protective mechanism of CLE and related signaling pathways for MIRI remains unclear. The objective of this study is to determine the mechanism by which CLE relieves MIRI in cardiomyocytes and its relationship with the TLR4/PI3K/Akt signaling pathway. CCK8 analysis was used to test the optimal concentration of TLR4 inhibitor CLI-095 and TLR4 agonist lipopolysaccharide (LPS) on MIRI. The expression of inflammatory factors, oxidative stress response, cell damage, and intracellular calcium redistribution of cardiomyocytes were examined using the ELISA kits, Total Superoxide Dismutase Assay Kit with WST-8 and Lipid Peroxidation MDA Assay Kit, LDH Cytotoxicity Assay Kit, and laser scanning confocal microscope. The expression of TLR4/PI3K/Akt and cleaved caspase-3 were determined by Western blotting and immunofluorescent staining. Our results showed that MIRI aggravated the inflammatory response, oxidative stress, cellular damage of cardiomyocytes, and caused redistribution of intracellular calcium, upregulated the expression of TLR4 protein, cleaved caspase-3 protein, and down-regulated the expression of PI3K/Akt protein. After treatment with CLE, the inflammatory response, oxidative stress, and cellular damage of cardiomyocytes were alleviated, and intracellular calcium ion accumulation decreased. The expression of TLR4 protein, cleaved caspase-3 protein declined, but PI3K/Akt protein expression increased in cardiomyocytes treated with CLE. In addition, after treatment with the TLR4 inhibitor CLI-095, the results were similar to those of CLE treatment. The TLR4 agonist LPS aggravated the reactions caused by MIRI. The role of LPS was reversed after CLE treatment. These results suggested that CLE can attenuate MIRI by activating the TLR4/PI3K/Akt signaling pathway.

Fabrication and evaluation of a regenerable HFO-doped agricultural waste for enhanced adsorption affinity towards phosphate.

Chemical modification of agricultural waste biomass has proved to be an economy and effective approach to capture phosphate ions, except for that under acidic conditions and highly competitive ion systems. According to this, a new nanocomposite (HFO@St+) was fabricated by incorporating nano-sized hydrous Fe(III) oxides (HFO) within aminated wheat straw in order to overcome the bottleneck. The optimal pH of phosphate uptake by HFO@St+ was greatly broadened and observed over a wide pH range between 2.0 and 7.0. The binary exchange reaction indicated that phosphate was strongly and preferably adsorbed by HFO@St+ with the separation factor K of phosphate over nitrate increasing from 0.23-1 or 0.20-0.26 to 2.5-38 or 2.5-15 for near neutral or acidic pHs, respectively. The sorption selectivity for HFO@St+ followed the order of phosphate > nitrate > chloride under experimental conditions. The presence of inorganic and organic ligands (SO4 and HA) showed no significant effect on phosphate adsorption. XPS and FT-IR analyses were performed to explore the underlying mechanism of adsorption. The exhausted material could be regenerated with NaOH-NaCl solution for at least ten cycles, indicating that HFO@St+ can be used as a sustainable biomass product with excellent adsorption affinity for phosphate removal.

Thermostable iron oxide nanoparticle synthesis within recombinant ferritins from the hyperthermophile Pyrococcus yayanosii CH1.

Thermostable nanoparticles have numerous applications in catalysis and in the oil/gas industry. However, synthesizing these nanoparticles requires expensive polymers. Here, a novel thermostable ferritin named PcFn, originally from the hyperthermophilic archaeon Pyrococcus yayanosii CH1, was overexpressed in Escherichia coli, purified and characterized, which could successfully direct the synthesis of thermostable magnetoferritins (M-PcFn) with monodispersed iron oxide nanoparticles in one step. Transmission electron microscopy and magnetic measurements show that the cores of the M-PcFn have an average diameter of 4.7 nm, are well-crystalline and superparamagnetic. Both the PcFn and M-PcFn can resist temperatures up to 110 °C, which is significantly higher than for human H-chain ferritin (HFn) and M-HFn, and comparable to temperatures previously reported for Pyrococcus furiosus ferritin (PfFn) and M-PfFn. After heating at 110 °C for 30 minutes, PcFn and M-PcFn maintained their secondary structures and PcFn retained 87.4% of its iron uptake activity. This remarkable thermostability of PcFn and M-PcFn suggests potential applications in elevated temperature environments.

Three-Dimensional Simulation of DRIE Process Based on the Narrow Band Level Set and Monte Carlo Method.

A three-dimensional topography simulation of deep reactive ion etching (DRIE) is developed based on the narrow band level set method for surface evolution and Monte Carlo method for flux distribution. The advanced level set method is implemented to simulate the time-related movements of etched surface. In the meanwhile, accelerated by ray tracing algorithm, the Monte Carlo method incorporates all dominant physical and chemical mechanisms such as ion-enhanced etching, ballistic transport, ion scattering, and sidewall passivation. The modified models of charged particles and neutral particles are epitomized to determine the contributions of etching rate. The effects such as scalloping effect and lag effect are investigated in simulations and experiments. Besides, the quantitative analyses are conducted to measure the simulation error. Finally, this simulator will be served as an accurate prediction tool for some MEMS fabrications.