scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets.

Undoubtedly, single-cell RNA sequencing (scRNA-seq) has changed the research landscape by providing insights into heterogeneous, complex and rare cell populations. Given that more such data sets will become available in the near future, their accurate assessment with compatible and robust models for cell type annotation is a prerequisite. Considering this, herein, we developed scAnno (scRNA-seq data annotation), an automated annotation tool for scRNA-seq data sets primarily based on the single-cell cluster levels, using a joint deconvolution strategy and logistic regression. We explicitly constructed a reference profile for human (30 cell types and 50 human tissues) and a reference profile for mouse (26 cell types and 50 mouse tissues) to support this novel methodology (scAnno). scAnno offers a possibility to obtain genes with high expression and specificity in a given cell type as cell type-specific genes (marker genes) by combining co-expression genes with seed genes as a core. Of importance, scAnno can accurately identify cell type-specific genes based on cell type reference expression profiles without any prior information. Particularly, in the peripheral blood mononuclear cell data set, the marker genes identified by scAnno showed cell type-specific expression, and the majority of marker genes matched exactly with those included in the CellMarker database. Besides validating the flexibility and interpretability of scAnno in identifying marker genes, we also proved its superiority in cell type annotation over other cell type annotation tools (SingleR, scPred, CHETAH and scmap-cluster) through internal validation of data sets (average annotation accuracy: 99.05%) and cross-platform data sets (average annotation accuracy: 95.56%). Taken together, we established the first novel methodology that utilizes a deconvolution strategy for automated cell typing and is capable of being a significant application in broader scRNA-seq analysis. scAnno is available at https://github.com/liuhong-jia/scAnno.

Energy-Efficient Co-production of Benzoquinone and H2 Using Waste Phenol in a Hybrid Alkali/Acid Flow Cell.

In both the manufacturing and chemical industries, benzoquinone is a crucial chemical product. A perfect and economical method for making benzoquinone is the electrochemical oxidation of phenol, thanks to the traditional thermal catalytic oxidation of phenol process requires high cost, serious pollution and harsh reaction conditions. Here, a unique heterostructure electrocatalyst on nickel foam (NF) consisting of nickel sulfide and nickel oxide (Ni9S8-Ni15O16/NF) was produced, and this catalyst exhibited a low overpotential (1.35 V vs. RHE) and prominent selectivity (99 %) for electrochemical phenol oxidation reaction (EOP). Ni9S8-Ni15O16/NF is beneficial for lowering the reaction energy barrier and boosting reactivity in the EOP process according to density functional theory (DFT) calculations. Additionally, an alkali/acid hybrid flow cell was successfully established by connecting Ni9S8-Ni15O16/NF and commercial RuIr/Ti in series to catalyze phenol oxidation in an alkaline medium and hydrogen evolution in an acid medium, respectively. A cell voltage of only 0.60 V was applied to produce a current density of 10 mA cm-2. Meanwhile, the system continued to operate at 0.90 V for 12 days, showing remarkable long-term stability. The unique configuration of the acid-base hybrid flow cell electrolyzer provides valuable guidance for the efficient and environmentally friendly electrooxidation of phenol to benzoquinone.

Insights into the trihelix transcription factor responses to salt and other stresses in Osmanthus fragrans.

BACKGROUND: Osmanthus fragrans is an evergreen plant with high ornamental and economic values. However, they are easily injured by salt stress, which severely limits their use in high salinity areas. The trihelix transcription factor (TF) family, as one of the earliest discovered TF families in plants, plays an essential part in responses to different abiotic stresses, and it has potential functions in improving the salt-tolerance capability of O. fragrans. RESULTS: In this study, 56 trihelix genes (OfGTs) were first identified in O. fragrans and then divided into five subfamilies in accordance with a phylogenetic tree analysis. The OfGTs were found to be located randomly on the 20 O. fragrans chromosomes, and an analysis of gene replication events indicated that the OfGT gene family underwent strong purification selection during the evolutionary process. The analysis of conserved motifs and gene structures implied that the OfGT members in the same subfamily have similar conserved motifs and gene structures. A promoter cis-elements analysis showed that all the OfGT genes contained multiple abiotic and hormonal stress-related cis-elements. The RNA-seq data suggested that the OfGTs have specific expression patterns in different tissues, and some were induced by salt stress. The qRT-PCR analysis of 12 selected OfGTs confirmed that OfGT1/3/21/33/42/45/46/52 were induced, with OfGT3/42/46 being the most highly expressed. In addition, OfGT42/OfGT46 had a co-expression pattern under salt-stress conditions. OfGT3/42/46 were mainly localized in the nuclei and exhibited no transcriptional activities based on the analysis of the subcellular localization and transcriptional activity assay. Furthermore, the expression levels of most of the selected OfGTs were induced by multiple abiotic and hormonal stresses, and the expression patterns of some OfGTs were also highly correlated with gibberellic acid and methyl jasmonate levels. Remarkably, the transient transformation results showed lower MDA content and increased expression of ROS-related genes NbAPX in transgenic plants, which implying OfGT3/42/46 may improve the salt tolerance of tobacco. CONCLUSIONS: The results implied that the OfGT genes were related to abiotic and hormonal stress responses in O. fragrans, and that the OfGT3/42/46 genes in particular might play crucial roles in responses to salt stress. This study made a comprehensive summary of the OfGT gene family, including functions and co-expression patterns in response to salt and other stresses, as well as an evolutionary perspective. Consequently, it lays a foundation for further functional characterizations of these genes.

A Visible Light Driven Photoelectrochemical Chloramphenicol Aptasensor Based on a Gold Nanoparticle-Functionalized 3D Flower-like MoS2/TiO2 Heterostructure.

Developing a photoactive material by combining the characteristics of a wide light response range and effective separation of photogenerated electron-hole pairs remains a huge challenge for the construction of a photoelectrochemical (PEC) sensing platform. Herein, a gold nanoparticle (AuNP)/MoS2/TiO2 composite was prepared through the facile hydrothermal method coupled with an in situ photoreduction technology. Benefiting from both the compositional and structure merits, the composite not only extends the absorption range to visible light but also enhances the photoelectric conversion efficiency by transferring photogenerated electrons into the conduction band of semiconductors from the plasmonic AuNP. Meanwhile, the thiolated aptamers were attached to the surface of AuNP/MoS2/TiO2 composites through the Au-S bonding to construct a visible light driven PEC aptasensor for ultrasensitive detection chloramphenicol (CAP). In the presence of CAP, the aptamers anchored on the surface of the photoactive materials could specifically recognize CAP and interact with it to form a bioaffinity complex with a steric hindrance effect, resulting in the rapid decrease of photocurrent responses. Based on this photocurrent suppression strategy, the constructed PEC aptasensing platform exhibited a high sensitivity with a wide linear range from 5 pM to 100 nM and a low detection limit of 0.5 pM.

[A review on integration methods for single-cell data].

The emergence of single-cell sequencing technology enables people to observe cells with unprecedented precision. However, it is difficult to capture the information on all cells and genes in one single-cell RNA sequencing (scRNA-seq) experiment. Single-cell data of a single modality cannot explain cell state and system changes in detail. The integrative analysis of single-cell data aims to address these two types of problems. Integrating multiple scRNA-seq data can collect complete cell types and provide a powerful boost for the construction of cell atlases. Integrating single-cell multimodal data can be used to study the causal relationship and gene regulation mechanism across modalities. The development and application of data integration methods helps fully explore the richness and relevance of single-cell data and discover meaningful biological changes. Based on this, this article reviews the basic principles, methods and applications of multiple scRNA-seq data integration and single-cell multimodal data integration. Moreover, the advantages and disadvantages of existing methods are discussed. Finally, the future development is prospected.

Laser with 10-13 short-term instability for compact optically pumped cesium beam atomic clock.

We realize a high-stability laser by modulation transfer spectroscopy and apply it to implement a high-performance compact optically pumped cesium beam atomic clock. Evaluated by the optical heterodyne method with two identical frequency-stabilized lasers, the frequency instability of the 852 nm laser directly referenced on thermal atoms is 2.6×10-13 at the averaging time of 5 s. Factors degrading the frequency stability of the laser are analyzed, and we will further control it to reduce the frequency noise of the laser. By comparing with a Hydrogen maser, the measured Allan deviation of the high-stability-laser-based cesium beam atomic clock is 2×10-12/τ, dropping to 1×10-14 in less than half a day of averaging time. To our knowledge, the Allan deviation of our cesium clock is better than that of any reported compact cesium beam atomic clocks at the averaging time of half-day. The high-performance atomic clock can promote the fields in metrology and timekeeping, and the high-stability laser additionally possesses great potential to be a compact optical frequency standard.

The Properties and Preparation Methods of Different Boron Nitride Nanostructures and Applications of Related Nanocomposites.

Due to special non-metallic polar bond between the III group (with certain metallic properties) element boron (B) and the V group element nitrogen (N), boron nitride (BN) has unique physical and chemical properties such as strong high-temperature resistance, oxidation resistance, heat conduction, electrical insulation and neutron absorption. Its unique lamellar, reticular and tubular morphologies and physicochemical properties make it attractive in the fields of adsorption, catalysis, hydrogen storage, thermal conduction, insulation, dielectric substrate of electronic devices, radiation protection, polymer composites, medicine, etc. Therefore, the synthesis and properties of BN derived materials become the main research hotspots of low-dimensional nanomaterials. This paper reviews the synthetic methods, overall properties, and applications of BN nanostructures and nanocomposites. In addition, challenges and prospect of this kind of materials are discussed.

Overview of Ionogels in Flexible Electronics.

Ionogels have aroused wide interests in the field of flexible electronics. The combination of solid-state networks and ionic liquids opens up thousands of possibilities for ionogels. The unique structures of ionogels endow them excellent mechanical properties, conductivity and thermal stability to approach the challenge of flexible electronic. A large number of new ionogels have been developed by different methods including the exchange of solution, polymeric ionic liquid and in-situ reactions in ionic liquids (gelation of low molecular weight gelators, self-assembly of block polymers, formation of double-network structure, ionogel nanocomposites and direct polymerization of polymerizable monomers). The aim of this review is to discuss different preparation methods of ionogels and the comparison of their advantages.

Research Progress in the Field of Adsorption and Catalytic Degradation of Sewage by Hydrotalcite-Derived Materials.

With the rapid development of industry and agriculture and the greatly improved living conditions, the resultant gradually deteriorated environments threaten the human beings. Refractory or even toxic pollutants, which are from different industries such as printing and dyeing, pesticides, chemicals, petrochemicals, plastics and rubber, seriously threat the ecosystems and human health. Having the advantages of flexible composition, unique structure, high stability, memory effect, easy preparation and low cost, hydrotalcite compounds have a great potential in sewage degradation and environmental protection. This study focuses on the adsorption and catalytic properties (such as photocatalysis, electrocatalysis and photoelectrocatalysis) of hydrotalcite-derived materials for treating organic, inorganic and heavy metal ion sewage. The types of adsorption and catalysis, and the effects of various influencing factors on the degradation efficiency were discussed as well.

Realization of phase locking in good-bad-cavity active optical clock.

The residual cavity-pulling effect limits further narrowing of linewidth in dual-wavelength (DW) good-bad-cavity active optical clocks (AOCs). In this paper, we for the first time experimentally realize the cavity-length stabilization of the 1064/1470 nm DW-AOCs by utilizing the phase locking technique of two independent 1064 nm good-cavity lasers. The frequency tracking accuracy between the two main-cavities of DW-AOCs is better than 3 × 10-16 at 1 s, and can reach 1 × 10-17 at 1000 s. Each 1470 nm bad-cavity laser achieves a most probable linewidth of 53 Hz, which is about a quarter of that without phase locking. The influence of the asynchronous cavity-lengths variation between two DW laser systems is suppressed.

Magnetically controlled capsule endoscopy as the first-line examination for high-risk patients for the standard gastroscopy: a preliminary study.

Background: Magnetically controlled capsule endoscopy (MCE) has emerged as a feasible and efficient diagnostic modality for gastric diseases. In a special group of patients, MCE may have an advantage over standard gastroscopy. Objective: This study aimed to evaluate the clinical utility of MCE in high-risk patients for standard gastroscopy. Methods: In this study, patients with high-risk factors for standard gastroscopy were examined by MCE between 1 January 2017 and 31 December 2017. The examination time, results, adverse events and clinical outcome were recorded. Results: Forty-two patients with high-risk factors for standard gastroscopy were enrolled in the present study. All patients successfully underwent MCE without any adverse events. Based on the findings from MCE, the patients were successfully treated. Conclusions: For patients with high-risk factors for standard gastroscopy, MCE could be the perfect alternative examination for gastric diseases. We recommend MCE as the first-line examination for high-risk patients, but its utility should be confirmed in further clinical studies.

Carbon Nanomaterials in Direct Liquid Fuel Cells.

Fuel cells have attracted more attentions due to many advantages they can provide, including high energy efficiency and low environmental burden. To form a stable, low cost and efficient catalyst, we presented here the state of the art of electrocatalyst fabrication approaches, involving carbon nanotubes and their multifunctional nanocomposites incorporated with noble metals, such as Pt, Pd, Au, their binary and ternary systems. Both fuel oxidation reactions and oxygen reduction reactions were emphasized with comprehensive examples and future prospects.

Dynamic flux balance analysis for microbial conversion of glycerol into 1,3-propanediol by Klebsiella pneumoniae.

To investigate the relationship between the yield of 1,3-propanediol (1,3-PD) and the flux variation in metabolic pathways of Klebsiella pneumoniae, an optimized calculation method was constructed on basis of dynamic flux balance analysis by combining genome-scale flux balance analysis with a kinetic model of extracellular metabolites. Through optimizing calculations, a more completely expanded metabolic pathway was obtained, which includes the previously reported metabolic pathway and additional three pathways or site: a pentose phosphate pathway (PPP) elicited at the dihydroxyacetone (DHA) node to provide more reducing equivalents; a branch of synthetic amino acids at the 3-phosphoglycerate (3PG) node; and the α-ketoglutarate site in the tricarboxylic acid (TCA) cycle leading to anabolic pathways for glutamate and other amino acids. On this basis, the relationships between the dynamic flux distribution of the important nodes in the metabolic pathway and the yield of 1,3-propanediol were analyzed. First, dynamic flux change from DHA to the PPP is positively correlated with the yield. Second, variation in flux in the TCA cycle is also positively correlated with the yield of 1,3-propanediol. In addition, the influence of the feedback loop formed by the cofactor tetrahydrofolate on the flux change of TCA in the amino acid anabolic pathway was examined. These results are of important reference value and have guiding significance for the extension of the glycerol metabolism pathway in K. pneumoniae, the rational transformation of genetic engineering in bacteria, and the optimization of metabolic pathways for industrial production.

Miniaturized calcium beam optical frequency standard using fully-sealed vacuum tube with 10-15 instability.

We implement a miniaturized calcium beam optical frequency standard using specially-designed fully-sealed vacuum tube, and realize the comparison with another calcium beam optical clock whose vacuum tube is sealed by flanges. The electron shelving detection method is adopted to improve the signal-to-noise ratio of the clock transition spectroscopy, and the readout laser is locked by modulation-free frequency locking technology based on Doppler effect. Injection locking is carried out to boost the power of the 657 nm master clock transition laser, thus ensuring the comparison. The fractional instability of the miniaturized calcium beam optical frequency standard using fully-sealed vacuum tube is 1.8×10-15 after 1600 s of averaging. Total volume of the system except for electronics is about 0.3 m3. To our knowledge, it's the first time to realize the optical frequency standard using fully-sealed vacuum tube. This work will promote the miniaturization and transportability of the optical clock based on atomic beam.

[Long-term effects of neonatal exposure to bisphenol A on testes structure and the expression of Boule in testes of male mice].

OBJECTIVE: To investigate the long-term effects and the mechanism of neonatal bisphenol A( BPA) exposure on mouse testicular structure and Boule expression. METHODS: A total of 12 pregnant ICR mice were randomly divided into three groups:blank control group, negative control group( corn oil) and BPA 100 µg/kg group. After delivery, BPA was given daily by neck subcutaneous injection to the offspring male mice from postnatal day( PND 1) to PND 21. The offspring male mice were sacrificed on PND35 and PND 70. Morphological changes of testes were detected with hematoxylin-eosin staining, the level of Boule mRNA expression was determined by RT-PCR, the expression of Boule protein was detected by immunofluorescence and Western blotting. RESULTS: Compared with blank control group and negative control group, the diameter and the epithelium thickness of seminiferous epithelium in the same period( PND 35, PND 70)were significantly decreased and the lumen was significantly increased( P < 0. 05) in the testes of BPA( 100 µg/kg) group. In addition, the expressions of Boule mRNA and protein were decreased remarkably( P < 0. 05, P < 0. 01) in testes of BPA 100 µg/kg group. CONCLUSION: Neonatal BPA exposure has a long-term effect on mouse testicular development and may affect testicular development by decreasing the expression of Boule mRNA and protein in testes.

Hanle detection for optical clocks.

Considering the strong inhomogeneous spatial polarization and intensity distribution of spontaneous decay fluorescence due to the Hanle effect, we propose and demonstrate a universe Hanle detection configuration of electron-shelving method for optical clocks. Experimental results from Ca atomic beam optical frequency standard with electron-shelving method show that a designed Hanle detection geometry with optimized magnetic field direction, detection laser beam propagation and polarization direction, and detector position can improve the fluorescence collection rate by more than one order of magnitude comparing with that of inefficient geometry. With the fixed 423 nm fluorescence, the improved 657 nm optical frequency standard signal intensity is presented. The potential application of the Hanle detection geometry designed for facilitating the fluorescence collection for optical lattice clock with a limited solid angle of the fluorescence collection has been discussed. The Hanle detection geometry is also effective for ion detection in ion optical clock and quantum information experiments. Besides, a cylinder fluorescence collection structure is designed to increase the solid angle of the fluorescence collection in Ca atomic beam optical frequency standard.

Kinetics-based development of two-stage continuous fermentation of 1,3-propanediol from crude glycerol by Clostridium butyricum.

BACKGROUND: Glycerol, as a by-product, mainly derives from the conversion of many crops to biodiesel, ethanol, and fatty ester. Its bioconversion to 1,3-propanediol (1,3-PDO) is an environmentally friendly method. Continuous fermentation has many striking merits over fed-batch and batch fermentation, such as high product concentration with easy feeding operation, long-term high productivity without frequent seed culture, and energy-intensive sterilization. However, it is usually difficult to harvest high product concentrations. RESULTS: In this study, a three-stage continuous fermentation was firstly designed to produce 1,3-PDO from crude glycerol by Clostridium butyricum, in which the first stage fermentation was responsible for providing the excellent cells in a robust growth state, the second stage focused on promoting 1,3-PDO production, and the third stage aimed to further boost the 1,3-PDO concentration and reduce the residual glycerol concentration as much as possible. Through the three-stage continuous fermentation, 80.05 g/L 1,3-PDO as the maximum concentration was produced while maintaining residual glycerol of 5.87 g/L, achieving a yield of 0.48 g/g and a productivity of 3.67 g/(L·h). Based on the 14 sets of experimental data from the first stage, a kinetic model was developed to describe the intricate relationships among the concentrations of 1,3-PDO, substrate, biomass, and butyrate. Subsequently, this kinetic model was used to optimize and predict the highest 1,3-PDO productivity of 11.26 g/(L·h) in the first stage fermentation, while the glycerol feeding concentration and dilution rate were determined to be 92 g/L and 0.341 h-1, separately. Additionally, to achieve a target 1,3-PDO production of 80 g/L without the third stage fermentation, the predicted minimum volume ratio of the second fermenter to the first one was 11.9. The kinetics-based two-stage continuous fermentation was experimentally verified well with the predicted results. CONCLUSION: A novel three-stage continuous fermentation and a kinetic model were reported. Then a simpler two-stage continuous fermentation was developed based on the optimization of the kinetic model. This kinetics-based development of two-stage continuous fermentation could achieve high-level production of 1,3-PDO. Meanwhile, it provides a reference for other bio-chemicals production by applying kinetics to optimize multi-stage continuous fermentation.

Dynamic flux balance analysis of 1,3-propanediol production by clostridium butyricum fermentation.

To study the relationship between the yield of 1,3-propanediol (1,3-PDO) and the flux change of the Clostridium butyricum metabolic pathway, an optimized calculation method based on dynamic flux balance analysis was used by combining genome-scale flux balance analysis with a kinetic model. A more comprehensive and extensive metabolic pathway was obtained by optimization calculations. The primary extended branches include: the dihydroxyacetone node, which enters the pentose phosphate pathway; the α-oxoglutarate node, which has synthetic metabolic pathways for glutamic acid and amino acids; and the serine and homocysteine nodes, which produce cystathionine before homocysteine enters the methionine cycle pathway. According to the expanded metabolic network, the flux distribution of key nodes in the metabolic pathway and the relationship between the flux distribution ratio of nodes and the yield of 1,3-PDO were analyzed. At the dihydroxyacetone node, the flux of dihydroxyacetone converted to dihydroxyacetone phosphate was positively correlated with the yield of 1,3-PDO. As an important intermediate product, the flux change in the metabolic pathway of α-oxoglutarate reacting with amino acids to produce glutamic acid is positively correlated with the yield. When pyruvate was used as the central node to convert into lactic acid and α-oxoglutarate, the proportion of branch flux was negatively correlated with the yield of 1,3-PDO. These studies provide a theoretical basis for the optimization and further study of the metabolic pathway of C. butyricum.

N-doped 3D carbon encapsulating nickel selenide nanoarchitecture with cation defect engineering: An ultrafast and long-life anode for sodium-ion batteries.

Transition metal chalcogenides (TMCs) hold great potential for sodium-ion batteries (SIBs) owing to their multielectron conversion reactions, yet face challenges of poor intrinsic conductivity, sluggish diffusion kinetics, severe phase transitions, and structural collapse during cycling. Herein, a self-templating strategy is proposed for the synthesis of a class of metal cobalt-doped NiSe nanoparticles confined within three-dimensional (3D) N-doped macroporous carbon matrix nanohybrids (Co-NiSe/NMC). The cation defect engineering within the developed Co-NiSe and 3D N-doped carbon plays a crucial role in enhancing intrinsic conductivity, reinforcing structural stability, and reducing the barrier to sodium ion diffusion, which are verified by a series of electrochemical kinetic analyses and density functional theory calculations. Significantly, such cation defect engineering not only reduces overpotential but also accelerates conversion reaction kinetics, ensuring both exceptional high-rate capability and extended durability. Consequently, the optimally engineered Co-NiSe/NMC demonstrates a remarkable rate performance, delivering 390 mAh g-1 at 10 A g-1. Moreover, it exhibits an unprecedented lifespan, maintaining a remarkable capacity of 403 mAh g-1 after 1400 cycles and 318 mAh g-1 after 4000 cycles, even at high rates of 1.0 and 2.0 A g-1, respectively. This work marks a substantial advancement in achieving both high performance and prolonged cycle life in sodium-ion batteries.